UKB ICD Immunedysregulation
Christopher Huebel
29/05/2019
autoimmune
Read in data
autoimmune <- fread(
input = "data_raw/2019_05_29_ICD/ICD10.autoimmune.txt",
header = TRUE,
stringsAsFactors = F,
data.table = F)
colnames(autoimmune)## [1] "IID" "D590m" "D590s" "IID" "D591m" "D591s" "IID"
## [8] "D613m" "IID" "D686m" "D686s" "IID" "D690m" "D690s"
## [15] "IID" "D693m" "D693s" "IID" "D70m" "D70s" "IID"
## [22] "D721m" "D721s" "IID" "D730s" "IID" "D731m" "D731s"
## [29] "IID" "D732m" "D732s" "IID" "D760m" "D760s" "IID"
## [36] "D761m" "D761s" "IID" "D860m" "D860s" "IID" "D861m"
## [43] "D861s" "IID" "D862m" "D862s" "IID" "D863m" "D863s"
## [50] "IID" "D868m" "D868s" "IID" "D869m" "D869s" "IID"
## [57] "D890m" "D890s" "IID" "D891m" "D891s" "IID" "D892m"
## [64] "D892s" "IID" "E05s" "IID" "E050m" "E050s" "IID"
## [71] "E063m" "E063s" "IID" "E100m" "E100s" "IID" "E101m"
## [78] "E101s" "IID" "E102m" "E102s" "IID" "E103m" "E103s"
## [85] "IID" "E104m" "E104s" "IID" "E105m" "E105s" "IID"
## [92] "E106m" "E106s" "IID" "E107m" "E107s" "IID" "E108m"
## [99] "E108s" "IID" "E109m" "E109s" "IID" "E121s" "IID"
## [106] "E128s" "IID" "E129s" "IID" "E208s" "IID" "E271m"
## [113] "E271s" "IID" "E283m" "E283s" "IID" "E310m" "E310s"
## [120] "IID" "E318m" "IID" "E319s" "IID" "E351s" "IID"
## [127] "G122m" "G122s" "IID" "G35m" "G35s" "IID" "G360m"
## [134] "G360s" "IID" "G368s" "IID" "G369m" "G369s" "IID"
## [141] "G370s" "IID" "G373m" "G373s" "IID" "G378m" "G378s"
## [148] "IID" "G379m" "G379s" "IID" "G610m" "G610s" "IID"
## [155] "G618m" "G618s" "IID" "G619m" "G619s" "IID" "G700m"
## [162] "G700s" "IID" "G724m" "G724s" "IID" "G731m" "G731s"
## [169] "IID" "H150m" "H150s" "IID" "H151m" "H151s" "IID"
## [176] "H201m" "H201s" "IID" "H208m" "H208s" "IID" "H209m"
## [183] "H209s" "IID" "H353m" "H353s" "IID" "I241m" "I241s"
## [190] "IID" "I730m" "I730s" "IID" "I731m" "I731s" "IID"
## [197] "I881m" "I881s" "IID" "K220m" "K220s" "IID" "K294m"
## [204] "K294s" "IID" "K500m" "K500s" "IID" "K501m" "K501s"
## [211] "IID" "K508m" "K508s" "IID" "K509m" "K509s" "IID"
## [218] "K510m" "K510s" "IID" "K511m" "K511s" "IID" "K512m"
## [225] "K512s" "IID" "K513m" "K513s" "IID" "K514m" "K514s"
## [232] "IID" "K515m" "K515s" "IID" "K518m" "K518s" "IID"
## [239] "K519m" "K519s" "IID" "K580m" "K580s" "IID" "K589m"
## [246] "K589s" "IID" "K721m" "K721s" "IID" "K754m" "K754s"
## [253] "IID" "K900m" "K900s" "IID" "L100m" "L100s" "IID"
## [260] "L102m" "L102s" "IID" "L104s" "IID" "L108m" "L108s"
## [267] "IID" "L109m" "L109s" "IID" "L110m" "L110s" "IID"
## [274] "L111m" "L111s" "IID" "L118m" "IID" "L119m" "L119s"
## [281] "IID" "L120m" "L120s" "IID" "L121m" "L121s" "IID"
## [288] "L123s" "IID" "L128m" "L128s" "IID" "L129m" "L129s"
## [295] "IID" "L130m" "L130s" "IID" "L131m" "L131s" "IID"
## [302] "L138m" "L138s" "IID" "L139m" "L139s" "IID" "L14s"
## [309] "IID" "L400m" "L400s" "IID" "L401m" "L401s" "IID"
## [316] "L403m" "L403s" "IID" "L404m" "L404s" "IID" "L405m"
## [323] "L405s" "IID" "L408m" "L408s" "IID" "L409m" "L409s"
## [330] "IID" "L410m" "L410s" "IID" "L430m" "L430s" "IID"
## [337] "L432m" "IID" "L433s" "IID" "L438m" "L438s" "IID"
## [344] "L439m" "L439s" "IID" "L441m" "L441s" "IID" "L443m"
## [351] "L443s" "IID" "L508m" "L508s" "IID" "L630m" "L630s"
## [358] "IID" "L631s" "IID" "L638m" "L638s" "IID" "L639m"
## [365] "L639s" "IID" "L80m" "L80s" "IID" "L930m" "L930s"
## [372] "IID" "L931m" "L931s" "IID" "L932m" "L932s" "IID"
## [379] "L940m" "L940s" "IID" "L941s" "IID" "M023m" "M023s"
## [386] "IID" "M0230m" "M0230s" "IID" "M0236m" "IID" "M0239m"
## [393] "M0239s" "IID" "M050m" "M050s" "IID" "M0500m" "M0500s"
## [400] "IID" "M0509m" "M0509s" "IID" "M051m" "M051s" "IID"
## [407] "M0510m" "M0510s" "IID" "M0518s" "IID" "M0519m" "M0519s"
## [414] "IID" "M052m" "M052s" "IID" "M0520m" "M0520s" "IID"
## [421] "M0524s" "IID" "M0526m" "IID" "M0528m" "M0528s" "IID"
## [428] "M0529m" "M0529s" "IID" "M053m" "M053s" "IID" "M0530m"
## [435] "M0530s" "IID" "M0538s" "IID" "M0539s" "IID" "M058m"
## [442] "M058s" "IID" "M0580m" "M0580s" "IID" "M0582m" "IID"
## [449] "M0583m" "IID" "M0584m" "M0584s" "IID" "M0586m" "IID"
## [456] "M0587m" "IID" "M0588m" "IID" "M0589m" "M0589s" "IID"
## [463] "M059m" "M059s" "IID" "M0590m" "M0590s" "IID" "M0591m"
## [470] "M0591s" "IID" "M0592m" "M0592s" "IID" "M0593m" "M0593s"
## [477] "IID" "M0594m" "M0594s" "IID" "M0595m" "M0595s" "IID"
## [484] "M0596m" "M0596s" "IID" "M0597m" "M0597s" "IID" "M0598m"
## [491] "M0598s" "IID" "M0599m" "M0599s" "IID" "M060m" "M060s"
## [498] "IID" "M0600m" "M0600s" "IID" "M0601m" "M0601s" "IID"
## [505] "M0602m" "M0602s" "IID" "M0603m" "M0603s" "IID" "M0604m"
## [512] "M0604s" "IID" "M0605m" "M0605s" "IID" "M0606m" "M0606s"
## [519] "IID" "M0607m" "M0607s" "IID" "M0608m" "IID" "M0609m"
## [526] "M0609s" "IID" "M061m" "M061s" "IID" "M0610m" "M0610s"
## [533] "IID" "M0611m" "IID" "M0616m" "IID" "M0619m" "M0619s"
## [540] "IID" "M062m" "M062s" "IID" "M0621m" "IID" "M0622m"
## [547] "IID" "M0625m" "IID" "M0627m" "IID" "M063m" "M063s"
## [554] "IID" "M0630m" "M0630s" "IID" "M0632m" "M0632s" "IID"
## [561] "M0633m" "M0633s" "IID" "M0634m" "M0634s" "IID" "M0636m"
## [568] "M0636s" "IID" "M0637m" "M0637s" "IID" "M0638m" "IID"
## [575] "M0639m" "IID" "M064m" "M064s" "IID" "M0640m" "M0640s"
## [582] "IID" "M0641m" "M0641s" "IID" "M0643m" "M0643s" "IID"
## [589] "M0644m" "IID" "M0645m" "M0645s" "IID" "M0646m" "M0646s"
## [596] "IID" "M0647m" "M0647s" "IID" "M0649m" "M0649s" "IID"
## [603] "M068m" "M068s" "IID" "M0680m" "M0680s" "IID" "M0681m"
## [610] "IID" "M0682m" "M0682s" "IID" "M0684s" "IID" "M0685m"
## [617] "IID" "M0686m" "IID" "M0687m" "IID" "M0688m" "IID"
## [624] "M0689m" "M0689s" "IID" "M069m" "M069s" "IID" "M0690m"
## [631] "M0690s" "IID" "M0691m" "M0691s" "IID" "M0692m" "M0692s"
## [638] "IID" "M0693m" "M0693s" "IID" "M0694m" "M0694s" "IID"
## [645] "M0695m" "M0695s" "IID" "M0696m" "M0696s" "IID" "M0697m"
## [652] "M0697s" "IID" "M0698m" "M0698s" "IID" "M0699m" "M0699s"
## [659] "IID" "M070s" "IID" "M0700s" "IID" "M0701s" "IID"
## [666] "M0703s" "IID" "M0704s" "IID" "M0707s" "IID" "M0709s"
## [673] "IID" "M071s" "IID" "M0719s" "IID" "M072s" "IID"
## [680] "M0726s" "IID" "M0728s" "IID" "M0729s" "IID" "M073m"
## [687] "M073s" "IID" "M0730m" "M0730s" "IID" "M0731s" "IID"
## [694] "M0732s" "IID" "M0733s" "IID" "M0734m" "M0734s" "IID"
## [701] "M0735m" "M0735s" "IID" "M0736m" "M0736s" "IID" "M0737m"
## [708] "M0737s" "IID" "M0738s" "IID" "M0739m" "M0739s" "IID"
## [715] "M074s" "IID" "M0740s" "IID" "M0746s" "IID" "M0747s"
## [722] "IID" "M0749s" "IID" "M075s" "IID" "M0750m" "M0750s"
## [729] "IID" "M0751m" "IID" "M0755s" "IID" "M0759s" "IID"
## [736] "M076m" "M076s" "IID" "M0760s" "IID" "M0764s" "IID"
## [743] "M0766m" "IID" "M0769s" "IID" "M080m" "M080s" "IID"
## [750] "M0800m" "M0800s" "IID" "M0802m" "IID" "M0805m" "IID"
## [757] "M0806m" "IID" "M0808m" "IID" "M0809m" "M0809s" "IID"
## [764] "M0810m" "M0810s" "IID" "M0819m" "M0819s" "IID" "M082m"
## [771] "M082s" "IID" "M0820s" "IID" "M0822m" "IID" "M0825s"
## [778] "IID" "M0826s" "IID" "M0828s" "IID" "M0829m" "M0829s"
## [785] "IID" "M0830m" "M0830s" "IID" "M0836m" "IID" "M0839s"
## [792] "IID" "M0840m" "M0840s" "IID" "M0844s" "IID" "M088s"
## [799] "IID" "M089m" "M089s" "IID" "M0890m" "M0890s" "IID"
## [806] "M0896m" "IID" "M0899m" "M0899s" "IID" "M300m" "M300s"
## [813] "IID" "M301m" "M301s" "IID" "M302m" "IID" "M303m"
## [820] "M303s" "IID" "M308m" "M308s" "IID" "M320m" "M320s"
## [827] "IID" "M321m" "M321s" "IID" "M328m" "M328s" "IID"
## [834] "M329m" "M329s" "IID" "M3290m" "M3290s" "IID" "M330s"
## [841] "IID" "M331m" "M331s" "IID" "M332m" "M332s" "IID"
## [848] "M339m" "M339s" "IID" "M340m" "M340s" "IID" "M341m"
## [855] "M341s" "IID" "M342m" "M342s" "IID" "M348m" "M348s"
## [862] "IID" "M349m" "M349s" "IID" "M350m" "M350s" "IID"
## [869] "M351m" "M351s" "IID" "M352m" "M352s" "IID" "M353m"
## [876] "M353s" "IID" "M354m" "M354s" "IID" "M355s" "IID"
## [883] "M357m" "M357s" "IID" "M358m" "M358s" "IID" "M359m"
## [890] "M359s" "IID" "M3599s" "IID" "M45m" "M45s" "IID"
## [897] "M45X0m" "M45X0s" "IID" "M45X1s" "IID" "M45X2m" "M45X2s"
## [904] "IID" "M45X4s" "IID" "M45X6m" "M45X6s" "IID" "M45X7m"
## [911] "M45X7s" "IID" "M45X8s" "IID" "M45X9m" "M45X9s" "IID"
## [918] "M600m" "M600s" "IID" "M6000m" "M6000s" "IID" "M6001m"
## [925] "M6001s" "IID" "M6002m" "IID" "M6003m" "IID" "M6005m"
## [932] "M6005s" "IID" "M6006m" "M6006s" "IID" "M6008m" "M6008s"
## [939] "IID" "M6009m" "IID" "M601s" "IID" "M6018s" "IID"
## [946] "M602m" "M602s" "IID" "M6021s" "IID" "M6023m" "M6023s"
## [953] "IID" "M6024m" "M6024s" "IID" "M6025m" "IID" "M6026s"
## [960] "IID" "M6027m" "IID" "M6028m" "M6028s" "IID" "M6029s"
## [967] "IID" "M608m" "M608s" "IID" "M6080m" "IID" "M6082m"
## [974] "IID" "M6085m" "IID" "M6086s" "IID" "M6088m" "IID"
## [981] "M6089m" "M6089s" "IID" "M609m" "M609s" "IID" "M6090m"
## [988] "M6090s" "IID" "M6091m" "M6091s" "IID" "M6092m" "M6092s"
## [995] "IID" "M6093m" "IID" "M6095m" "M6095s" "IID" "M6096m"
## [1002] "M6096s" "IID" "M6097m" "IID" "M6098m" "M6098s" "IID"
## [1009] "M6099m" "M6099s" "IID" "N030m" "N030s" "IID" "N031m"
## [1016] "N031s" "IID" "N032m" "N032s" "IID" "N033m" "N033s"
## [1023] "IID" "N035m" "N035s" "IID" "N036m" "N036s" "IID"
## [1030] "N037m" "N037s" "IID" "N038m" "N038s" "IID" "N039m"
## [1037] "N039s" "IID" "N050m" "N050s" "IID" "N051m" "N051s"
## [1044] "IID" "N052m" "N052s" "IID" "N053m" "N053s" "IID"
## [1051] "N054m" "N054s" "IID" "N055m" "N055s" "IID" "N056m"
## [1058] "N056s" "IID" "N057m" "N057s" "IID" "N058m" "N058s"
## [1065] "IID" "N059m" "N059s" "IID" "N301m" "N301s" "IID"
## [1072] "N711m" "N711s" "IID" "O264s"Remove duplicate column
autoimmune_no_duplicate <- autoimmune[!duplicated(as.list(autoimmune))]
colnames(autoimmune_no_duplicate)## [1] "IID" "D590m" "D590s" "D591m" "D591s" "D613m" "D686m"
## [8] "D686s" "D690m" "D690s" "D693m" "D693s" "D70m" "D70s"
## [15] "D721m" "D721s" "D730s" "D731m" "D731s" "D732m" "D732s"
## [22] "D760m" "D760s" "D761m" "D761s" "D860m" "D860s" "D861m"
## [29] "D861s" "D862m" "D862s" "D863m" "D863s" "D868m" "D868s"
## [36] "D869m" "D869s" "D890m" "D890s" "D891m" "D891s" "D892m"
## [43] "D892s" "E05s" "E050m" "E050s" "E063m" "E063s" "E100m"
## [50] "E100s" "E101m" "E101s" "E102m" "E102s" "E103m" "E103s"
## [57] "E104m" "E104s" "E105m" "E105s" "E106m" "E106s" "E107m"
## [64] "E107s" "E108m" "E108s" "E109m" "E109s" "E121s" "E128s"
## [71] "E129s" "E208s" "E271m" "E271s" "E283m" "E283s" "E310m"
## [78] "E310s" "E318m" "E319s" "E351s" "G122m" "G122s" "G35m"
## [85] "G35s" "G360m" "G360s" "G368s" "G369m" "G369s" "G370s"
## [92] "G373m" "G373s" "G378m" "G378s" "G379m" "G379s" "G610m"
## [99] "G610s" "G618m" "G618s" "G619m" "G619s" "G700m" "G700s"
## [106] "G724m" "G724s" "G731m" "G731s" "H150m" "H150s" "H151m"
## [113] "H151s" "H201m" "H201s" "H208m" "H208s" "H209m" "H209s"
## [120] "H353m" "H353s" "I241m" "I241s" "I730m" "I730s" "I731m"
## [127] "I731s" "I881m" "I881s" "K220m" "K220s" "K294m" "K294s"
## [134] "K500m" "K500s" "K501m" "K501s" "K508m" "K508s" "K509m"
## [141] "K509s" "K510m" "K510s" "K511m" "K511s" "K512m" "K512s"
## [148] "K513m" "K513s" "K514m" "K514s" "K515m" "K515s" "K518m"
## [155] "K518s" "K519m" "K519s" "K580m" "K580s" "K589m" "K589s"
## [162] "K721m" "K721s" "K754m" "K754s" "K900m" "K900s" "L100m"
## [169] "L100s" "L102m" "L102s" "L104s" "L108m" "L108s" "L109m"
## [176] "L109s" "L110m" "L110s" "L111m" "L111s" "L118m" "L119m"
## [183] "L119s" "L120m" "L120s" "L121m" "L121s" "L123s" "L128m"
## [190] "L128s" "L129m" "L129s" "L130m" "L130s" "L131m" "L131s"
## [197] "L138m" "L138s" "L139m" "L139s" "L14s" "L400m" "L400s"
## [204] "L401m" "L401s" "L403m" "L403s" "L404m" "L404s" "L405m"
## [211] "L405s" "L408m" "L408s" "L409m" "L409s" "L410m" "L410s"
## [218] "L430m" "L430s" "L432m" "L433s" "L438m" "L438s" "L439m"
## [225] "L439s" "L441m" "L441s" "L443m" "L443s" "L508m" "L508s"
## [232] "L630m" "L630s" "L631s" "L638m" "L638s" "L639m" "L639s"
## [239] "L80m" "L80s" "L930m" "L930s" "L931m" "L931s" "L932m"
## [246] "L932s" "L940m" "L940s" "L941s" "M023m" "M023s" "M0230m"
## [253] "M0230s" "M0236m" "M0239m" "M0239s" "M050m" "M050s" "M0500m"
## [260] "M0500s" "M0509m" "M0509s" "M051m" "M051s" "M0510m" "M0510s"
## [267] "M0518s" "M0519m" "M0519s" "M052m" "M052s" "M0520m" "M0520s"
## [274] "M0524s" "M0526m" "M0528m" "M0528s" "M0529m" "M0529s" "M053m"
## [281] "M053s" "M0538s" "M0539s" "M058m" "M058s" "M0580m" "M0580s"
## [288] "M0582m" "M0583m" "M0584m" "M0584s" "M0586m" "M0587m" "M0588m"
## [295] "M0589m" "M0589s" "M059m" "M059s" "M0590m" "M0590s" "M0591m"
## [302] "M0591s" "M0592m" "M0592s" "M0593m" "M0593s" "M0594m" "M0594s"
## [309] "M0595m" "M0595s" "M0596m" "M0596s" "M0597m" "M0597s" "M0598m"
## [316] "M0598s" "M0599m" "M0599s" "M060m" "M060s" "M0600m" "M0600s"
## [323] "M0601m" "M0601s" "M0602m" "M0602s" "M0603m" "M0603s" "M0604m"
## [330] "M0604s" "M0605m" "M0605s" "M0606m" "M0606s" "M0607m" "M0607s"
## [337] "M0608m" "M0609m" "M0609s" "M061m" "M061s" "M0610m" "M0610s"
## [344] "M0611m" "M0616m" "M0619m" "M0619s" "M062m" "M062s" "M0621m"
## [351] "M0622m" "M0625m" "M0627m" "M063m" "M063s" "M0630m" "M0630s"
## [358] "M0632m" "M0632s" "M0633m" "M0633s" "M0634m" "M0634s" "M0636m"
## [365] "M0636s" "M0637m" "M0637s" "M0638m" "M0639m" "M064m" "M064s"
## [372] "M0640m" "M0640s" "M0641m" "M0641s" "M0643m" "M0643s" "M0644m"
## [379] "M0645m" "M0645s" "M0646m" "M0646s" "M0647m" "M0649m" "M0649s"
## [386] "M068m" "M068s" "M0680m" "M0680s" "M0681m" "M0682m" "M0682s"
## [393] "M0684s" "M0685m" "M0686m" "M0687m" "M0688m" "M0689m" "M0689s"
## [400] "M069m" "M069s" "M0690m" "M0690s" "M0691m" "M0691s" "M0692m"
## [407] "M0692s" "M0693m" "M0693s" "M0694m" "M0694s" "M0695m" "M0695s"
## [414] "M0696m" "M0696s" "M0697m" "M0697s" "M0698m" "M0698s" "M0699m"
## [421] "M0699s" "M070s" "M0700s" "M0701s" "M0703s" "M0704s" "M0707s"
## [428] "M0709s" "M071s" "M0719s" "M072s" "M0726s" "M0728s" "M0729s"
## [435] "M073m" "M073s" "M0730m" "M0730s" "M0731s" "M0732s" "M0733s"
## [442] "M0734m" "M0734s" "M0735m" "M0735s" "M0736m" "M0736s" "M0737m"
## [449] "M0737s" "M0738s" "M0739m" "M0739s" "M074s" "M0740s" "M0746s"
## [456] "M0749s" "M075s" "M0750m" "M0750s" "M0751m" "M0755s" "M0759s"
## [463] "M076m" "M076s" "M0760s" "M0766m" "M0769s" "M080m" "M080s"
## [470] "M0800m" "M0800s" "M0802m" "M0805m" "M0806m" "M0808m" "M0809s"
## [477] "M0810m" "M0819m" "M0819s" "M082m" "M082s" "M0820s" "M0825s"
## [484] "M0826s" "M0828s" "M0829m" "M0829s" "M0830m" "M0830s" "M0836m"
## [491] "M0839s" "M0840m" "M0840s" "M0844s" "M088s" "M089m" "M089s"
## [498] "M0890m" "M0890s" "M0899m" "M0899s" "M300m" "M300s" "M301m"
## [505] "M301s" "M302m" "M303m" "M303s" "M308m" "M308s" "M320m"
## [512] "M320s" "M321m" "M321s" "M328m" "M328s" "M329m" "M329s"
## [519] "M3290m" "M3290s" "M330s" "M331m" "M331s" "M332m" "M332s"
## [526] "M339m" "M339s" "M340m" "M340s" "M341m" "M341s" "M342m"
## [533] "M342s" "M348m" "M348s" "M349m" "M349s" "M350m" "M350s"
## [540] "M351m" "M351s" "M352m" "M352s" "M353m" "M353s" "M354m"
## [547] "M354s" "M355s" "M357m" "M357s" "M358m" "M358s" "M359m"
## [554] "M359s" "M3599s" "M45m" "M45s" "M45X0m" "M45X0s" "M45X1s"
## [561] "M45X2m" "M45X2s" "M45X4s" "M45X6m" "M45X6s" "M45X7m" "M45X7s"
## [568] "M45X8s" "M45X9m" "M45X9s" "M600m" "M600s" "M6000m" "M6000s"
## [575] "M6001m" "M6001s" "M6002m" "M6005m" "M6005s" "M6006m" "M6006s"
## [582] "M6008m" "M6008s" "M6009m" "M601s" "M6018s" "M602m" "M602s"
## [589] "M6021s" "M6023m" "M6023s" "M6024m" "M6024s" "M6025m" "M6026s"
## [596] "M6027m" "M6028m" "M6028s" "M6029s" "M608m" "M608s" "M6080m"
## [603] "M6082m" "M6085m" "M6086s" "M6088m" "M6089m" "M6089s" "M609m"
## [610] "M609s" "M6090m" "M6090s" "M6091m" "M6091s" "M6092m" "M6092s"
## [617] "M6093m" "M6095m" "M6095s" "M6096m" "M6096s" "M6097m" "M6098m"
## [624] "M6098s" "M6099m" "M6099s" "N030m" "N030s" "N031m" "N031s"
## [631] "N032m" "N032s" "N033m" "N033s" "N035m" "N035s" "N036m"
## [638] "N037m" "N037s" "N038m" "N038s" "N039m" "N039s" "N050m"
## [645] "N050s" "N051m" "N051s" "N052m" "N052s" "N053m" "N053s"
## [652] "N054m" "N054s" "N055m" "N055s" "N056m" "N056s" "N057m"
## [659] "N057s" "N058m" "N058s" "N059m" "N059s" "N301m" "N301s"
## [666] "N711m" "N711s" "O264s"Create summary column
autoimmune_no_duplicate$ICD.autoimmune.raw <-
apply(
autoimmune_no_duplicate[,2:ncol(autoimmune_no_duplicate)] == 1,
1,
any)
autoimmune_no_duplicate$ICD.autoimmune <-
as.integer(
autoimmune_no_duplicate$ICD.autoimmune.raw
)
autoimmune_reduced <- autoimmune_no_duplicate %>%
select(IID, ICD.autoimmune)Summary
summary(as.factor(autoimmune_reduced$ICD.autoimmune))## 0 1
## 460600 42019autoinflammatory
Read in data
autoinflammatory <- fread(
input = "data_raw/2019_05_29_ICD/ICD10.autoinflammatory.txt",
header = TRUE,
stringsAsFactors = F,
data.table = F)
colnames(autoinflammatory)## [1] "IID" "A150m" "A150s" "IID" "A151m" "A151s" "IID"
## [8] "A152m" "A152s" "IID" "A153m" "A153s" "IID" "A154s"
## [15] "IID" "A155s" "IID" "A156m" "A156s" "IID" "A157m"
## [22] "A157s" "IID" "A159m" "A159s" "IID" "A160m" "A160s"
## [29] "IID" "A161s" "IID" "A162m" "A162s" "IID" "A163m"
## [36] "A163s" "IID" "A164m" "A164s" "IID" "A165m" "A165s"
## [43] "IID" "A167s" "IID" "A169m" "A169s" "IID" "A170m"
## [50] "A170s" "IID" "A178m" "A178s" "IID" "A180m" "A180s"
## [57] "IID" "A181m" "A181s" "IID" "A182m" "A182s" "IID"
## [64] "A183m" "A183s" "IID" "A184m" "A184s" "IID" "A185m"
## [71] "A185s" "IID" "A187m" "A187s" "IID" "A188m" "A188s"
## [78] "IID" "A190m" "IID" "A192m" "IID" "A199m" "A199s"
## [85] "IID" "B159m" "B159s" "IID" "B160m" "IID" "B169m"
## [92] "B169s" "IID" "B171m" "B171s" "IID" "B172m" "B172s"
## [99] "IID" "B178m" "B178s" "IID" "B179m" "B179s" "IID"
## [106] "B180m" "B180s" "IID" "B181m" "B181s" "IID" "B182m"
## [113] "B182s" "IID" "B188m" "B188s" "IID" "B189m" "B189s"
## [120] "IID" "B199m" "B199s" "IID" "B200m" "IID" "B201m"
## [127] "IID" "B202m" "B202s" "IID" "B203m" "B203s" "IID"
## [134] "B204m" "B204s" "IID" "B206m" "B206s" "IID" "B207m"
## [141] "B207s" "IID" "B208m" "B208s" "IID" "B210m" "B210s"
## [148] "IID" "B211m" "IID" "B212m" "B212s" "IID" "B213m"
## [155] "B213s" "IID" "B217m" "IID" "B218m" "IID" "B220m"
## [162] "B220s" "IID" "B221m" "B221s" "IID" "B222m" "IID"
## [169] "B227m" "B227s" "IID" "B230m" "B230s" "IID" "B232m"
## [176] "B232s" "IID" "B238m" "B238s" "IID" "B24m" "B24s"
## [183] "IID" "C000m" "IID" "C001m" "C001s" "IID" "C002m"
## [190] "IID" "C003m" "IID" "C004m" "C004s" "IID" "C005s"
## [197] "IID" "C006m" "IID" "C009m" "C009s" "IID" "C01m"
## [204] "C01s" "IID" "C020m" "C020s" "IID" "C021m" "C021s"
## [211] "IID" "C022m" "C022s" "IID" "C023m" "C023s" "IID"
## [218] "C024m" "C024s" "IID" "C028m" "C028s" "IID" "C029m"
## [225] "C029s" "IID" "C030m" "IID" "C031m" "C031s" "IID"
## [232] "C039m" "C039s" "IID" "C040m" "C040s" "IID" "C041m"
## [239] "C041s" "IID" "C048m" "IID" "C049m" "C049s" "IID"
## [246] "C050m" "IID" "C051m" "C051s" "IID" "C052m" "IID"
## [253] "C058m" "IID" "C059m" "C059s" "IID" "C060m" "C060s"
## [260] "IID" "C061m" "IID" "C062m" "C062s" "IID" "C068m"
## [267] "C068s" "IID" "C069m" "C069s" "IID" "C07m" "C07s"
## [274] "IID" "C080m" "C080s" "IID" "C081m" "IID" "C088m"
## [281] "IID" "C089m" "C089s" "IID" "C090m" "C090s" "IID"
## [288] "C091m" "C091s" "IID" "C098m" "IID" "C099m" "C099s"
## [295] "IID" "C100m" "C100s" "IID" "C102m" "IID" "C103m"
## [302] "C103s" "IID" "C104m" "C104s" "IID" "C108m" "C108s"
## [309] "IID" "C109m" "C109s" "IID" "C110m" "IID" "C111m"
## [316] "C111s" "IID" "C112m" "C112s" "IID" "C113m" "C113s"
## [323] "IID" "C119m" "C119s" "IID" "C12m" "C12s" "IID"
## [330] "C130m" "C130s" "IID" "C131m" "IID" "C132s" "IID"
## [337] "C138m" "IID" "C139m" "C139s" "IID" "C140m" "C140s"
## [344] "IID" "C148m" "C148s" "IID" "C150m" "C150s" "IID"
## [351] "C151m" "C151s" "IID" "C152m" "C152s" "IID" "C153m"
## [358] "C153s" "IID" "C154m" "C154s" "IID" "C155m" "C155s"
## [365] "IID" "C158m" "C158s" "IID" "C159m" "C159s" "IID"
## [372] "C160m" "C160s" "IID" "C161m" "C161s" "IID" "C162m"
## [379] "C162s" "IID" "C163m" "C163s" "IID" "C164m" "C164s"
## [386] "IID" "C165m" "C165s" "IID" "C166m" "C166s" "IID"
## [393] "C168m" "C168s" "IID" "C169m" "C169s" "IID" "C170m"
## [400] "C170s" "IID" "C171m" "C171s" "IID" "C172m" "C172s"
## [407] "IID" "C173m" "C173s" "IID" "C178m" "C178s" "IID"
## [414] "C179m" "C179s" "IID" "C180m" "C180s" "IID" "C181m"
## [421] "C181s" "IID" "C182m" "C182s" "IID" "C183m" "C183s"
## [428] "IID" "C184m" "C184s" "IID" "C185m" "C185s" "IID"
## [435] "C186m" "C186s" "IID" "C187m" "C187s" "IID" "C188m"
## [442] "C188s" "IID" "C189m" "C189s" "IID" "C19m" "C19s"
## [449] "IID" "C20m" "C20s" "IID" "C210m" "C210s" "IID"
## [456] "C211m" "C211s" "IID" "C218m" "C218s" "IID" "C220m"
## [463] "C220s" "IID" "C221m" "C221s" "IID" "C222s" "IID"
## [470] "C223m" "C223s" "IID" "C224m" "C224s" "IID" "C227m"
## [477] "C227s" "IID" "C229m" "C229s" "IID" "C23m" "C23s"
## [484] "IID" "C240m" "C240s" "IID" "C241m" "C241s" "IID"
## [491] "C248m" "C248s" "IID" "C249m" "C249s" "IID" "C250m"
## [498] "C250s" "IID" "C251m" "C251s" "IID" "C252m" "C252s"
## [505] "IID" "C253m" "C253s" "IID" "C254m" "C254s" "IID"
## [512] "C257m" "C257s" "IID" "C258m" "C258s" "IID" "C259m"
## [519] "C259s" "IID" "C260m" "C260s" "IID" "C261m" "C261s"
## [526] "IID" "C268m" "C268s" "IID" "C269m" "C269s" "IID"
## [533] "C300m" "C300s" "IID" "C301m" "IID" "C310m" "C310s"
## [540] "IID" "C311m" "C311s" "IID" "C312m" "IID" "C313m"
## [547] "IID" "C318s" "IID" "C319m" "C319s" "IID" "C320m"
## [554] "C320s" "IID" "C321m" "C321s" "IID" "C322m" "C322s"
## [561] "IID" "C323m" "C323s" "IID" "C328m" "IID" "C329m"
## [568] "C329s" "IID" "C33m" "C33s" "IID" "C340m" "C340s"
## [575] "IID" "C341m" "C341s" "IID" "C342m" "C342s" "IID"
## [582] "C343m" "C343s" "IID" "C348m" "C348s" "IID" "C349m"
## [589] "C349s" "IID" "C37m" "C37s" "IID" "C380m" "IID"
## [596] "C381m" "C381s" "IID" "C382m" "IID" "C383m" "C383s"
## [603] "IID" "C384m" "C384s" "IID" "C390m" "IID" "C399s"
## [610] "IID" "C400m" "C400s" "IID" "C401m" "C401s" "IID"
## [617] "C402m" "C402s" "IID" "C403m" "C403s" "IID" "C408m"
## [624] "IID" "C410m" "C410s" "IID" "C411m" "C411s" "IID"
## [631] "C412m" "C412s" "IID" "C413m" "C413s" "IID" "C414m"
## [638] "C414s" "IID" "C419m" "C419s" "IID" "C430m" "IID"
## [645] "C431m" "IID" "C432m" "C432s" "IID" "C433m" "C433s"
## [652] "IID" "C434m" "C434s" "IID" "C435m" "C435s" "IID"
## [659] "C436m" "C436s" "IID" "C437m" "C437s" "IID" "C438m"
## [666] "IID" "C439m" "C439s" "IID" "C440m" "C440s" "IID"
## [673] "C441m" "C441s" "IID" "C442m" "C442s" "IID" "C443m"
## [680] "C443s" "IID" "C444m" "C444s" "IID" "C445m" "C445s"
## [687] "IID" "C446m" "C446s" "IID" "C447m" "C447s" "IID"
## [694] "C448m" "C448s" "IID" "C449m" "C449s" "IID" "C450m"
## [701] "C450s" "IID" "C451m" "C451s" "IID" "C457m" "C457s"
## [708] "IID" "C459m" "C459s" "IID" "C460m" "C460s" "IID"
## [715] "C461s" "IID" "C462s" "IID" "C463m" "C463s" "IID"
## [722] "C467m" "C467s" "IID" "C468s" "IID" "C469m" "C469s"
## [729] "IID" "C470m" "C470s" "IID" "C471m" "C471s" "IID"
## [736] "C472m" "IID" "C473m" "C473s" "IID" "C474s" "IID"
## [743] "C475m" "C475s" "IID" "C476m" "IID" "C479m" "C479s"
## [750] "IID" "C480m" "C480s" "IID" "C481m" "C481s" "IID"
## [757] "C482m" "C482s" "IID" "C488m" "IID" "C490m" "C490s"
## [764] "IID" "C491m" "C491s" "IID" "C492m" "C492s" "IID"
## [771] "C493m" "C493s" "IID" "C494m" "C494s" "IID" "C495m"
## [778] "C495s" "IID" "C496m" "C496s" "IID" "C498m" "C498s"
## [785] "IID" "C499m" "C499s" "IID" "C500m" "C500s" "IID"
## [792] "C501m" "C501s" "IID" "C502m" "C502s" "IID" "C503m"
## [799] "C503s" "IID" "C504m" "C504s" "IID" "C505m" "C505s"
## [806] "IID" "C506m" "C506s" "IID" "C508m" "C508s" "IID"
## [813] "C509m" "C509s" "IID" "C510m" "C510s" "IID" "C511m"
## [820] "C511s" "IID" "C512s" "IID" "C518m" "IID" "C519m"
## [827] "C519s" "IID" "C52m" "C52s" "IID" "C530m" "C530s"
## [834] "IID" "C531m" "IID" "C538m" "C538s" "IID" "C539m"
## [841] "C539s" "IID" "C540m" "C540s" "IID" "C541m" "C541s"
## [848] "IID" "C542m" "IID" "C543m" "IID" "C548m" "IID"
## [855] "C549m" "C549s" "IID" "C55m" "C55s" "IID" "C56m"
## [862] "C56s" "IID" "C570m" "C570s" "IID" "C571m" "IID"
## [869] "C574m" "IID" "C577m" "C577s" "IID" "C578m" "C578s"
## [876] "IID" "C579m" "C579s" "IID" "C58m" "IID" "C600m"
## [883] "C600s" "IID" "C601m" "C601s" "IID" "C602m" "C602s"
## [890] "IID" "C608m" "IID" "C609m" "C609s" "IID" "C61m"
## [897] "C61s" "IID" "C620m" "IID" "C621m" "C621s" "IID"
## [904] "C629m" "C629s" "IID" "C631m" "IID" "C632m" "C632s"
## [911] "IID" "C637m" "IID" "C639m" "IID" "C64m" "C64s"
## [918] "IID" "C65m" "C65s" "IID" "C66m" "C66s" "IID"
## [925] "C670m" "C670s" "IID" "C671m" "C671s" "IID" "C672m"
## [932] "C672s" "IID" "C673m" "C673s" "IID" "C674m" "C674s"
## [939] "IID" "C675m" "C675s" "IID" "C676m" "C676s" "IID"
## [946] "C677m" "C677s" "IID" "C678m" "C678s" "IID" "C679m"
## [953] "C679s" "IID" "C680m" "C680s" "IID" "C688m" "IID"
## [960] "C689m" "C689s" "IID" "C690m" "IID" "C691m" "IID"
## [967] "C692m" "C692s" "IID" "C693m" "C693s" "IID" "C694m"
## [974] "C694s" "IID" "C695m" "C695s" "IID" "C696m" "C696s"
## [981] "IID" "C698m" "IID" "C699m" "C699s" "IID" "C700m"
## [988] "C700s" "IID" "C701m" "C701s" "IID" "C709m" "C709s"
## [995] "IID" "C710m" "C710s" "IID" "C711m" "C711s" "IID"
## [1002] "C712m" "C712s" "IID" "C713m" "C713s" "IID" "C714m"
## [1009] "C714s" "IID" "C715m" "C715s" "IID" "C716m" "C716s"
## [1016] "IID" "C717m" "C717s" "IID" "C718m" "C718s" "IID"
## [1023] "C719m" "C719s" "IID" "C720m" "C720s" "IID" "C721m"
## [1030] "C721s" "IID" "C722m" "C722s" "IID" "C724m" "IID"
## [1037] "C725m" "IID" "C728m" "IID" "C729m" "IID" "C73m"
## [1044] "C73s" "IID" "C740m" "C740s" "IID" "C741m" "C741s"
## [1051] "IID" "C749m" "C749s" "IID" "C750m" "C750s" "IID"
## [1058] "C751m" "C751s" "IID" "C752s" "IID" "C753s" "IID"
## [1065] "C755m" "C755s" "IID" "C759m" "C759s" "IID" "D000m"
## [1072] "D000s" "IID" "D001m" "D001s" "IID" "D002m" "D002s"
## [1079] "IID" "D010m" "D010s" "IID" "D012m" "D012s" "IID"
## [1086] "D013m" "D013s" "IID" "D015m" "D015s" "IID" "D017m"
## [1093] "IID" "D020m" "D020s" "IID" "D021m" "D021s" "IID"
## [1100] "D022m" "D022s" "IID" "D023m" "D023s" "IID" "D030m"
## [1107] "IID" "D031m" "D031s" "IID" "D032m" "D032s" "IID"
## [1114] "D033m" "D033s" "IID" "D034m" "D034s" "IID" "D035m"
## [1121] "D035s" "IID" "D036m" "D036s" "IID" "D037m" "D037s"
## [1128] "IID" "D038m" "D038s" "IID" "D039m" "D039s" "IID"
## [1135] "D040m" "IID" "D041m" "D041s" "IID" "D042m" "D042s"
## [1142] "IID" "D043m" "D043s" "IID" "D044m" "D044s" "IID"
## [1149] "D045m" "D045s" "IID" "D046m" "D046s" "IID" "D047m"
## [1156] "D047s" "IID" "D048m" "D048s" "IID" "D049m" "D049s"
## [1163] "IID" "D050m" "D050s" "IID" "D051m" "D051s" "IID"
## [1170] "D057m" "D057s" "IID" "D059m" "D059s" "IID" "D060m"
## [1177] "D060s" "IID" "D061m" "D061s" "IID" "D067m" "D067s"
## [1184] "IID" "D069m" "D069s" "IID" "D070m" "IID" "D071m"
## [1191] "D071s" "IID" "D072m" "D072s" "IID" "D073m" "D073s"
## [1198] "IID" "D074m" "D074s" "IID" "D075m" "D075s" "IID"
## [1205] "D076m" "D076s" "IID" "D090m" "D090s" "IID" "D091m"
## [1212] "D091s" "IID" "D092m" "IID" "D093m" "D093s" "IID"
## [1219] "D097m" "IID" "D099m" "D099s" "IID" "D70m" "D70s"
## [1226] "IID" "D71m" "D71s" "IID" "D721m" "D721s" "IID"
## [1233] "D728m" "D728s" "IID" "D729m" "D729s" "IID" "D730s"
## [1240] "IID" "D731m" "D731s" "IID" "D732m" "D732s" "IID"
## [1247] "D733m" "D733s" "IID" "D734m" "D734s" "IID" "D735m"
## [1254] "D735s" "IID" "D748s" "IID" "D749s" "IID" "D750m"
## [1261] "D750s" "IID" "D751m" "D751s" "IID" "D752m" "D752s"
## [1268] "IID" "D758m" "D758s" "IID" "D759m" "D759s" "IID"
## [1275] "D760m" "D760s" "IID" "D761m" "D761s" "IID" "D762s"
## [1282] "IID" "D763m" "D763s" "IID" "D77s" "IID" "D860m"
## [1289] "D860s" "IID" "D861m" "D861s" "IID" "D862m" "D862s"
## [1296] "IID" "D863m" "D863s" "IID" "D868m" "D868s" "IID"
## [1303] "D869m" "D869s" "IID" "D890m" "D890s" "IID" "D891m"
## [1310] "D891s" "IID" "D892m" "D892s" "IID" "D898m" "D898s"
## [1317] "IID" "D899m" "D899s" "IID" "E05s" "IID" "E051m"
## [1324] "E051s" "IID" "E052m" "E052s" "IID" "E053m" "E053s"
## [1331] "IID" "E054s" "IID" "E055m" "E055s" "IID" "E058m"
## [1338] "E058s" "IID" "E059m" "E059s" "IID" "E060m" "IID"
## [1345] "E062m" "E062s" "IID" "E064m" "E064s" "IID" "E065m"
## [1352] "E065s" "IID" "E069m" "E069s" "IID" "E110m" "E110s"
## [1359] "IID" "E111m" "E111s" "IID" "E112m" "E112s" "IID"
## [1366] "E113m" "E113s" "IID" "E114m" "E114s" "IID" "E115m"
## [1373] "E115s" "IID" "E116m" "E116s" "IID" "E117m" "E117s"
## [1380] "IID" "E118m" "E118s" "IID" "E119m" "E119s" "IID"
## [1387] "E121s" "IID" "E128s" "IID" "E129s" "IID" "E230m"
## [1394] "E230s" "IID" "E231m" "E231s" "IID" "E236m" "E236s"
## [1401] "IID" "E237m" "E237s" "IID" "E282m" "E282s" "IID"
## [1408] "E320m" "E320s" "IID" "E328m" "E328s" "IID" "E329m"
## [1415] "E329s" "IID" "E340m" "E340s" "IID" "E351s" "IID"
## [1422] "E840m" "E840s" "IID" "E841m" "E841s" "IID" "E848m"
## [1429] "E848s" "IID" "E849m" "E849s" "IID" "G031m" "G031s"
## [1436] "IID" "G032m" "G032s" "IID" "G618m" "G618s" "IID"
## [1443] "G619m" "G619s" "IID" "G724m" "G724s" "IID" "H044m"
## [1450] "H044s" "IID" "H051m" "H051s" "IID" "H150m" "H150s"
## [1457] "IID" "H151m" "H151s" "IID" "H163m" "H163s" "IID"
## [1464] "H200m" "H200s" "IID" "H201m" "H201s" "IID" "H202m"
## [1471] "H202s" "IID" "H208m" "H208s" "IID" "H209m" "H209s"
## [1478] "IID" "H353m" "H353s" "IID" "H652m" "H652s" "IID"
## [1485] "H653m" "H653s" "IID" "H654m" "H654s" "IID" "H661m"
## [1492] "H661s" "IID" "H662m" "H662s" "IID" "H663m" "H663s"
## [1499] "IID" "H701m" "H701s" "IID" "H731m" "H731s" "IID"
## [1506] "H912m" "H912s" "IID" "I050m" "I050s" "IID" "I051m"
## [1513] "I051s" "IID" "I052m" "I052s" "IID" "I058m" "I058s"
## [1520] "IID" "I059m" "I059s" "IID" "I060m" "I060s" "IID"
## [1527] "I061m" "I061s" "IID" "I062m" "I062s" "IID" "I068s"
## [1534] "IID" "I069m" "I069s" "IID" "I070m" "I070s" "IID"
## [1541] "I071m" "I071s" "IID" "I072s" "IID" "I078m" "I078s"
## [1548] "IID" "I079s" "IID" "I080m" "I080s" "IID" "I081m"
## [1555] "I081s" "IID" "I082m" "I082s" "IID" "I083m" "I083s"
## [1562] "IID" "I088m" "I088s" "IID" "I089m" "I089s" "IID"
## [1569] "I091m" "I091s" "IID" "I098m" "IID" "I099m" "I099s"
## [1576] "IID" "I241m" "I241s" "IID" "I418s" "IID" "I731m"
## [1583] "I731s" "IID" "I881m" "I881s" "IID" "J310m" "J310s"
## [1590] "IID" "J311m" "J311s" "IID" "J312m" "J312s" "IID"
## [1597] "J320m" "J320s" "IID" "J321m" "J321s" "IID" "J322m"
## [1604] "J322s" "IID" "J323m" "J323s" "IID" "J324m" "J324s"
## [1611] "IID" "J328m" "J328s" "IID" "J329m" "J329s" "IID"
## [1618] "J350m" "J350s" "IID" "J351m" "J351s" "IID" "J352m"
## [1625] "J352s" "IID" "J353m" "IID" "J358m" "J358s" "IID"
## [1632] "J359m" "J359s" "IID" "J370m" "J370s" "IID" "J40m"
## [1639] "J40s" "IID" "J410m" "J410s" "IID" "J411m" "IID"
## [1646] "J42m" "J42s" "IID" "J430m" "J430s" "IID" "J431m"
## [1653] "J431s" "IID" "J432m" "J432s" "IID" "J438m" "J438s"
## [1660] "IID" "J439m" "J439s" "IID" "J440m" "J440s" "IID"
## [1667] "J441m" "J441s" "IID" "J448m" "J448s" "IID" "J449m"
## [1674] "J449s" "IID" "J450m" "J450s" "IID" "J451m" "J451s"
## [1681] "IID" "J458m" "J458s" "IID" "J459m" "J459s" "IID"
## [1688] "J46m" "J46s" "IID" "J47m" "J47s" "IID" "J840m"
## [1695] "J840s" "IID" "J841m" "J841s" "IID" "J848m" "J848s"
## [1702] "IID" "J849m" "J849s" "IID" "K033m" "K033s" "IID"
## [1709] "K040m" "K040s" "IID" "K044m" "K044s" "IID" "K045m"
## [1716] "K045s" "IID" "K046m" "K046s" "IID" "K047m" "K047s"
## [1723] "IID" "K050m" "K050s" "IID" "K051m" "K051s" "IID"
## [1730] "K052m" "K052s" "IID" "K0522s" "IID" "K053m" "K053s"
## [1737] "IID" "K054m" "K054s" "IID" "K055m" "K055s" "IID"
## [1744] "K056m" "K056s" "IID" "K090m" "K090s" "IID" "K091m"
## [1751] "K091s" "IID" "K092m" "K092s" "IID" "K098m" "K098s"
## [1758] "IID" "K099m" "K099s" "IID" "K102m" "K102s" "IID"
## [1765] "K103m" "K103s" "IID" "K112m" "K112s" "IID" "K121m"
## [1772] "K121s" "IID" "K122m" "K122s" "IID" "K123m" "K123s"
## [1779] "IID" "K140m" "K140s" "IID" "K220m" "K220s" "IID"
## [1786] "K227m" "K227s" "IID" "K254m" "K254s" "IID" "K255m"
## [1793] "K255s" "IID" "K256m" "K256s" "IID" "K257m" "K257s"
## [1800] "IID" "K264m" "K264s" "IID" "K265m" "K265s" "IID"
## [1807] "K266m" "K266s" "IID" "K267m" "K267s" "IID" "K274m"
## [1814] "K274s" "IID" "K275m" "K275s" "IID" "K276m" "K276s"
## [1821] "IID" "K277m" "K277s" "IID" "K284m" "IID" "K285m"
## [1828] "IID" "K286m" "IID" "K287m" "K287s" "IID" "K292m"
## [1835] "K292s" "IID" "K293m" "K293s" "IID" "K294m" "K294s"
## [1842] "IID" "K295m" "K295s" "IID" "K296m" "K296s" "IID"
## [1849] "K500m" "K500s" "IID" "K501m" "K501s" "IID" "K508m"
## [1856] "K508s" "IID" "K509m" "K509s" "IID" "K510m" "K510s"
## [1863] "IID" "K511m" "K511s" "IID" "K512m" "K512s" "IID"
## [1870] "K513m" "K513s" "IID" "K514m" "K514s" "IID" "K515m"
## [1877] "K515s" "IID" "K518m" "K518s" "IID" "K519m" "K519s"
## [1884] "IID" "K520m" "K520s" "IID" "K521m" "K521s" "IID"
## [1891] "K522m" "K522s" "IID" "K523m" "K523s" "IID" "K528m"
## [1898] "K528s" "IID" "K529m" "K529s" "IID" "K580m" "K580s"
## [1905] "IID" "K589m" "K589s" "IID" "K601m" "K601s" "IID"
## [1912] "K700m" "K700s" "IID" "K701m" "K701s" "IID" "K702m"
## [1919] "K702s" "IID" "K703m" "K703s" "IID" "K704m" "K704s"
## [1926] "IID" "K709m" "K709s" "IID" "K710m" "K710s" "IID"
## [1933] "K711m" "K711s" "IID" "K712m" "K712s" "IID" "K713s"
## [1940] "IID" "K715m" "IID" "K716m" "K716s" "IID" "K717m"
## [1947] "K717s" "IID" "K718m" "K718s" "IID" "K719m" "K719s"
## [1954] "IID" "K720m" "K720s" "IID" "K721m" "K721s" "IID"
## [1961] "K729m" "K729s" "IID" "K730m" "IID" "K731m" "K731s"
## [1968] "IID" "K732m" "K732s" "IID" "K738m" "K738s" "IID"
## [1975] "K739m" "K739s" "IID" "K740m" "K740s" "IID" "K741m"
## [1982] "K741s" "IID" "K742m" "K742s" "IID" "K743m" "K743s"
## [1989] "IID" "K744m" "K744s" "IID" "K745m" "K745s" "IID"
## [1996] "K746m" "K746s" "IID" "K750m" "K750s" "IID" "K751s"
## [2003] "IID" "K752m" "K752s" "IID" "K753m" "K753s" "IID"
## [2010] "K754m" "K754s" "IID" "K758m" "K758s" "IID" "K759m"
## [2017] "K759s" "IID" "K760m" "K760s" "IID" "K761m" "K761s"
## [2024] "IID" "K762m" "K762s" "IID" "K763m" "K763s" "IID"
## [2031] "K765s" "IID" "K766m" "K766s" "IID" "K767m" "K767s"
## [2038] "IID" "K768m" "K768s" "IID" "K769m" "K769s" "IID"
## [2045] "K770m" "K770s" "IID" "K778s" "IID" "K811m" "K811s"
## [2052] "IID" "K830m" "K830s" "IID" "K860m" "K860s" "IID"
## [2059] "K861m" "K861s" "IID" "K900m" "K900s" "IID" "L410m"
## [2066] "L410s" "IID" "M300m" "M300s" "IID" "M301m" "M301s"
## [2073] "IID" "M302m" "IID" "M303m" "M303s" "IID" "M308m"
## [2080] "M308s" "IID" "M310m" "M310s" "IID" "M311m" "M311s"
## [2087] "IID" "M312s" "IID" "M313m" "M313s" "IID" "M314m"
## [2094] "M314s" "IID" "M315m" "M315s" "IID" "M316m" "M316s"
## [2101] "IID" "M317m" "M317s" "IID" "M318m" "M318s" "IID"
## [2108] "M319m" "M319s" "IID" "M320m" "M320s" "IID" "M321m"
## [2115] "M321s" "IID" "M328m" "M328s" "IID" "M329m" "M329s"
## [2122] "IID" "M3290m" "M3290s" "IID" "M330s" "IID" "M331m"
## [2129] "M331s" "IID" "M332m" "M332s" "IID" "M339m" "M339s"
## [2136] "IID" "M350m" "M350s" "IID" "M351m" "M351s" "IID"
## [2143] "M352m" "M352s" "IID" "M353m" "M353s" "IID" "M354m"
## [2150] "M354s" "IID" "M355s" "IID" "M357m" "M357s" "IID"
## [2157] "M358m" "M358s" "IID" "M359m" "M359s" "IID" "M3599s"
## [2164] "IID" "M360m" "M360s" "IID" "M362s" "IID" "M364s"
## [2171] "IID" "M368s" "IID" "M461m" "M461s" "IID" "M4616m"
## [2178] "M4616s" "IID" "M4617m" "M4617s" "IID" "M4618m" "M4618s"
## [2185] "IID" "M4619m" "M4619s" "IID" "M600m" "M600s" "IID"
## [2192] "M6000m" "M6000s" "IID" "M6001m" "M6001s" "IID" "M6002m"
## [2199] "IID" "M6003m" "IID" "M6005m" "M6005s" "IID" "M6006m"
## [2206] "M6006s" "IID" "M6008m" "M6008s" "IID" "M6009m" "IID"
## [2213] "M601s" "IID" "M6018s" "IID" "M602m" "M602s" "IID"
## [2220] "M6021s" "IID" "M6023m" "M6023s" "IID" "M6024m" "M6024s"
## [2227] "IID" "M6025m" "IID" "M6026s" "IID" "M6027m" "IID"
## [2234] "M6028m" "M6028s" "IID" "M6029s" "IID" "M608m" "M608s"
## [2241] "IID" "M6080m" "IID" "M6082m" "IID" "M6085m" "IID"
## [2248] "M6086s" "IID" "M6088m" "IID" "M6089m" "M6089s" "IID"
## [2255] "M609m" "M609s" "IID" "M6090m" "M6090s" "IID" "M6091m"
## [2262] "M6091s" "IID" "M6092m" "M6092s" "IID" "M6093m" "IID"
## [2269] "M6095m" "M6095s" "IID" "M6096m" "M6096s" "IID" "M6097m"
## [2276] "IID" "M6098m" "M6098s" "IID" "M6099m" "M6099s" "IID"
## [2283] "M610m" "IID" "M6106m" "IID" "M6114s" "IID" "M6115m"
## [2290] "IID" "M6125s" "IID" "M613s" "IID" "M614m" "M614s"
## [2297] "IID" "M615m" "M615s" "IID" "M6150s" "IID" "M6152m"
## [2304] "IID" "M6155m" "M6155s" "IID" "M6156m" "M6156s" "IID"
## [2311] "M6158s" "IID" "M6159m" "IID" "M619m" "M619s" "IID"
## [2318] "M6190s" "IID" "M6191s" "IID" "M6192s" "IID" "M6195m"
## [2325] "IID" "M6196s" "IID" "M6198s" "IID" "M632s" "IID"
## [2332] "M633s" "IID" "M638s" "IID" "M863m" "IID" "M8630m"
## [2339] "IID" "N001m" "N001s" "IID" "N002s" "IID" "N004s"
## [2346] "IID" "N005m" "IID" "N007s" "IID" "N008m" "N008s"
## [2353] "IID" "N009m" "N009s" "IID" "N015s" "IID" "N017m"
## [2360] "N017s" "IID" "N019m" "N019s" "IID" "N030m" "N030s"
## [2367] "IID" "N031m" "N031s" "IID" "N032m" "N032s" "IID"
## [2374] "N033m" "N033s" "IID" "N035m" "N035s" "IID" "N036m"
## [2381] "N036s" "IID" "N037m" "N037s" "IID" "N038m" "N038s"
## [2388] "IID" "N039m" "N039s" "IID" "N050m" "N050s" "IID"
## [2395] "N051m" "N051s" "IID" "N052m" "N052s" "IID" "N053m"
## [2402] "N053s" "IID" "N054m" "N054s" "IID" "N055m" "N055s"
## [2409] "IID" "N056m" "N056s" "IID" "N057m" "N057s" "IID"
## [2416] "N058m" "N058s" "IID" "N059m" "N059s" "IID" "N301m"
## [2423] "N301s" "IID" "N411m" "N411s" "IID" "N701m" "N701s"
## [2430] "IID" "N711m" "N711s" "IID" "N731m" "N731s" "IID"
## [2437] "N734s" "IID" "N761m" "N761s"Remove duplicate column
autoinflammatory_no_duplicate <- autoinflammatory[!duplicated(as.list(autoinflammatory))]
colnames(autoinflammatory_no_duplicate)## [1] "IID" "A150m" "A150s" "A151m" "A151s" "A152m" "A152s"
## [8] "A153m" "A153s" "A154s" "A155s" "A156m" "A156s" "A157m"
## [15] "A157s" "A159m" "A159s" "A160m" "A160s" "A161s" "A162m"
## [22] "A162s" "A163m" "A163s" "A164m" "A165m" "A165s" "A167s"
## [29] "A169m" "A169s" "A170m" "A170s" "A178m" "A178s" "A180m"
## [36] "A180s" "A181m" "A181s" "A182m" "A182s" "A183m" "A183s"
## [43] "A184m" "A184s" "A185m" "A187m" "A187s" "A188m" "A188s"
## [50] "A190m" "A192m" "A199m" "A199s" "B159m" "B159s" "B160m"
## [57] "B169m" "B169s" "B171m" "B171s" "B172m" "B172s" "B178m"
## [64] "B178s" "B179m" "B179s" "B180m" "B180s" "B181m" "B181s"
## [71] "B182m" "B182s" "B188m" "B188s" "B189m" "B189s" "B199m"
## [78] "B199s" "B200m" "B201m" "B202m" "B202s" "B203m" "B203s"
## [85] "B204m" "B204s" "B206m" "B206s" "B207m" "B207s" "B208m"
## [92] "B208s" "B210m" "B210s" "B211m" "B212m" "B212s" "B213m"
## [99] "B213s" "B217m" "B218m" "B220m" "B220s" "B221m" "B221s"
## [106] "B222m" "B227m" "B227s" "B230m" "B230s" "B232m" "B232s"
## [113] "B238m" "B238s" "B24m" "B24s" "C000m" "C001m" "C001s"
## [120] "C002m" "C003m" "C004m" "C005s" "C006m" "C009m" "C009s"
## [127] "C01m" "C01s" "C020m" "C020s" "C021m" "C021s" "C022m"
## [134] "C022s" "C023m" "C023s" "C024m" "C024s" "C028m" "C028s"
## [141] "C029m" "C029s" "C030m" "C031m" "C031s" "C039m" "C039s"
## [148] "C040m" "C040s" "C041m" "C041s" "C048m" "C049m" "C049s"
## [155] "C050m" "C051m" "C051s" "C052m" "C058m" "C059m" "C059s"
## [162] "C060m" "C060s" "C061m" "C062m" "C062s" "C068m" "C068s"
## [169] "C069m" "C069s" "C07m" "C07s" "C080m" "C080s" "C081m"
## [176] "C088m" "C089m" "C089s" "C090m" "C090s" "C091m" "C091s"
## [183] "C098m" "C099m" "C099s" "C100m" "C100s" "C102m" "C103m"
## [190] "C103s" "C104m" "C104s" "C108m" "C108s" "C109m" "C109s"
## [197] "C110m" "C111m" "C111s" "C112m" "C113m" "C113s" "C119m"
## [204] "C119s" "C12m" "C12s" "C130m" "C130s" "C131m" "C132s"
## [211] "C138m" "C139m" "C139s" "C140m" "C140s" "C148m" "C148s"
## [218] "C150m" "C150s" "C151m" "C151s" "C152m" "C152s" "C153m"
## [225] "C153s" "C154m" "C154s" "C155m" "C155s" "C158m" "C158s"
## [232] "C159m" "C159s" "C160m" "C160s" "C161m" "C161s" "C162m"
## [239] "C162s" "C163m" "C163s" "C164m" "C164s" "C165m" "C165s"
## [246] "C166m" "C166s" "C168m" "C168s" "C169m" "C169s" "C170m"
## [253] "C170s" "C171m" "C171s" "C172m" "C172s" "C173m" "C173s"
## [260] "C178m" "C178s" "C179m" "C179s" "C180m" "C180s" "C181m"
## [267] "C181s" "C182m" "C182s" "C183m" "C183s" "C184m" "C184s"
## [274] "C185m" "C185s" "C186m" "C186s" "C187m" "C187s" "C188m"
## [281] "C188s" "C189m" "C189s" "C19m" "C19s" "C20m" "C20s"
## [288] "C210m" "C210s" "C211m" "C211s" "C218m" "C218s" "C220m"
## [295] "C220s" "C221m" "C221s" "C222s" "C223m" "C223s" "C224m"
## [302] "C224s" "C227m" "C227s" "C229m" "C229s" "C23m" "C23s"
## [309] "C240m" "C240s" "C241m" "C241s" "C248m" "C248s" "C249m"
## [316] "C249s" "C250m" "C250s" "C251m" "C251s" "C252m" "C252s"
## [323] "C253m" "C253s" "C254m" "C254s" "C257m" "C257s" "C258m"
## [330] "C258s" "C259m" "C259s" "C260m" "C260s" "C261m" "C261s"
## [337] "C268m" "C268s" "C269m" "C269s" "C300m" "C300s" "C301m"
## [344] "C310m" "C310s" "C311m" "C311s" "C312m" "C313m" "C318s"
## [351] "C319m" "C319s" "C320m" "C320s" "C321m" "C321s" "C322m"
## [358] "C322s" "C323m" "C323s" "C328m" "C329m" "C329s" "C33m"
## [365] "C33s" "C340m" "C340s" "C341m" "C341s" "C342m" "C342s"
## [372] "C343m" "C343s" "C348m" "C348s" "C349m" "C349s" "C37m"
## [379] "C37s" "C380m" "C381m" "C381s" "C382m" "C383m" "C383s"
## [386] "C384m" "C384s" "C390m" "C399s" "C400m" "C400s" "C401m"
## [393] "C401s" "C402m" "C402s" "C403m" "C403s" "C408m" "C410m"
## [400] "C410s" "C411m" "C411s" "C412m" "C412s" "C413m" "C413s"
## [407] "C414m" "C414s" "C419m" "C419s" "C430m" "C431m" "C432m"
## [414] "C432s" "C433m" "C433s" "C434m" "C434s" "C435m" "C435s"
## [421] "C436m" "C436s" "C437m" "C437s" "C438m" "C439m" "C439s"
## [428] "C440m" "C440s" "C441m" "C441s" "C442m" "C442s" "C443m"
## [435] "C443s" "C444m" "C444s" "C445m" "C445s" "C446m" "C446s"
## [442] "C447m" "C447s" "C448m" "C448s" "C449m" "C449s" "C450m"
## [449] "C450s" "C451m" "C451s" "C457m" "C457s" "C459m" "C459s"
## [456] "C460m" "C460s" "C461s" "C462s" "C463s" "C467s" "C469m"
## [463] "C469s" "C470m" "C470s" "C471m" "C471s" "C472m" "C473m"
## [470] "C473s" "C474s" "C475m" "C475s" "C476m" "C479m" "C479s"
## [477] "C480m" "C480s" "C481m" "C481s" "C482m" "C482s" "C488m"
## [484] "C490m" "C490s" "C491m" "C491s" "C492m" "C492s" "C493m"
## [491] "C493s" "C494m" "C494s" "C495m" "C495s" "C496m" "C496s"
## [498] "C498m" "C498s" "C499m" "C499s" "C500m" "C500s" "C501m"
## [505] "C501s" "C502m" "C502s" "C503m" "C503s" "C504m" "C504s"
## [512] "C505m" "C505s" "C506m" "C506s" "C508m" "C508s" "C509m"
## [519] "C509s" "C510m" "C510s" "C511m" "C511s" "C512s" "C518m"
## [526] "C519m" "C519s" "C52m" "C52s" "C530m" "C530s" "C531m"
## [533] "C538m" "C538s" "C539m" "C539s" "C540m" "C540s" "C541m"
## [540] "C541s" "C542m" "C543m" "C548m" "C549m" "C549s" "C55m"
## [547] "C55s" "C56m" "C56s" "C570m" "C570s" "C571m" "C574m"
## [554] "C577m" "C577s" "C578m" "C578s" "C579m" "C579s" "C58m"
## [561] "C600m" "C600s" "C601m" "C601s" "C602m" "C602s" "C608m"
## [568] "C609m" "C609s" "C61m" "C61s" "C620m" "C621m" "C621s"
## [575] "C629m" "C629s" "C631m" "C632m" "C632s" "C637m" "C639m"
## [582] "C64m" "C64s" "C65m" "C65s" "C66m" "C66s" "C670m"
## [589] "C670s" "C671m" "C671s" "C672m" "C672s" "C673m" "C673s"
## [596] "C674m" "C674s" "C675m" "C675s" "C676m" "C676s" "C677m"
## [603] "C677s" "C678m" "C678s" "C679m" "C679s" "C680m" "C680s"
## [610] "C688m" "C689m" "C689s" "C690m" "C691m" "C692m" "C692s"
## [617] "C693m" "C693s" "C694m" "C694s" "C695m" "C695s" "C696m"
## [624] "C696s" "C698m" "C699m" "C699s" "C700m" "C700s" "C701m"
## [631] "C701s" "C709m" "C709s" "C710m" "C710s" "C711m" "C711s"
## [638] "C712m" "C712s" "C713m" "C713s" "C714m" "C714s" "C715m"
## [645] "C715s" "C716m" "C716s" "C717m" "C717s" "C718m" "C718s"
## [652] "C719m" "C719s" "C720m" "C720s" "C721m" "C721s" "C722m"
## [659] "C722s" "C724m" "C725m" "C728m" "C729m" "C73m" "C73s"
## [666] "C740m" "C740s" "C741m" "C741s" "C749m" "C749s" "C750m"
## [673] "C750s" "C751m" "C751s" "C752s" "C753s" "C755m" "C755s"
## [680] "C759m" "C759s" "D000m" "D000s" "D001m" "D001s" "D002m"
## [687] "D002s" "D010m" "D010s" "D012m" "D012s" "D013m" "D013s"
## [694] "D015m" "D015s" "D017m" "D020m" "D020s" "D021m" "D021s"
## [701] "D022m" "D022s" "D023m" "D023s" "D030m" "D031m" "D031s"
## [708] "D032m" "D032s" "D033m" "D033s" "D034m" "D034s" "D035m"
## [715] "D035s" "D036m" "D036s" "D037m" "D037s" "D038m" "D038s"
## [722] "D039m" "D039s" "D040m" "D041m" "D041s" "D042m" "D042s"
## [729] "D043m" "D043s" "D044m" "D044s" "D045m" "D045s" "D046m"
## [736] "D046s" "D047m" "D047s" "D048m" "D048s" "D049m" "D049s"
## [743] "D050m" "D050s" "D051m" "D051s" "D057m" "D057s" "D059m"
## [750] "D059s" "D060m" "D060s" "D061m" "D061s" "D067m" "D067s"
## [757] "D069m" "D069s" "D070m" "D071m" "D071s" "D072m" "D072s"
## [764] "D073m" "D073s" "D074m" "D074s" "D075m" "D075s" "D076m"
## [771] "D076s" "D090m" "D090s" "D091m" "D091s" "D092m" "D093m"
## [778] "D093s" "D097m" "D099m" "D099s" "D70m" "D70s" "D71m"
## [785] "D71s" "D721m" "D721s" "D728m" "D728s" "D729m" "D729s"
## [792] "D730s" "D731m" "D731s" "D732m" "D732s" "D733m" "D733s"
## [799] "D734m" "D734s" "D735m" "D735s" "D748s" "D749s" "D750m"
## [806] "D750s" "D751m" "D751s" "D752m" "D752s" "D758m" "D758s"
## [813] "D759m" "D759s" "D760m" "D760s" "D761m" "D761s" "D762s"
## [820] "D763m" "D763s" "D77s" "D860m" "D860s" "D861m" "D861s"
## [827] "D862m" "D862s" "D863m" "D863s" "D868m" "D868s" "D869m"
## [834] "D869s" "D890m" "D890s" "D891m" "D891s" "D892m" "D892s"
## [841] "D898m" "D898s" "D899m" "D899s" "E05s" "E051m" "E051s"
## [848] "E052m" "E052s" "E053m" "E053s" "E054s" "E055m" "E055s"
## [855] "E058m" "E058s" "E059m" "E059s" "E060m" "E062m" "E062s"
## [862] "E064m" "E064s" "E065m" "E065s" "E069m" "E069s" "E110m"
## [869] "E110s" "E111m" "E111s" "E112m" "E112s" "E113m" "E113s"
## [876] "E114m" "E114s" "E115m" "E115s" "E116m" "E116s" "E117m"
## [883] "E117s" "E118m" "E118s" "E119m" "E119s" "E121s" "E128s"
## [890] "E129s" "E230m" "E230s" "E231m" "E231s" "E236m" "E236s"
## [897] "E237m" "E237s" "E282m" "E282s" "E320m" "E320s" "E328m"
## [904] "E328s" "E329m" "E329s" "E340m" "E340s" "E351s" "E840m"
## [911] "E840s" "E841m" "E841s" "E848m" "E848s" "E849m" "E849s"
## [918] "G031m" "G031s" "G032m" "G032s" "G618m" "G618s" "G619m"
## [925] "G619s" "G724m" "G724s" "H044m" "H044s" "H051m" "H051s"
## [932] "H150m" "H150s" "H151m" "H151s" "H163m" "H163s" "H200m"
## [939] "H200s" "H201m" "H201s" "H202m" "H202s" "H208m" "H208s"
## [946] "H209m" "H209s" "H353m" "H353s" "H652m" "H652s" "H653m"
## [953] "H653s" "H654m" "H654s" "H661m" "H661s" "H662m" "H662s"
## [960] "H663m" "H663s" "H701m" "H701s" "H731m" "H731s" "H912m"
## [967] "H912s" "I050m" "I050s" "I051m" "I051s" "I052m" "I052s"
## [974] "I058m" "I058s" "I059m" "I059s" "I060m" "I060s" "I061m"
## [981] "I061s" "I062m" "I062s" "I068s" "I069m" "I069s" "I070m"
## [988] "I070s" "I071m" "I071s" "I072s" "I078m" "I078s" "I079s"
## [995] "I080m" "I080s" "I081m" "I081s" "I082m" "I082s" "I083m"
## [1002] "I083s" "I088m" "I088s" "I089m" "I089s" "I091m" "I091s"
## [1009] "I098m" "I099m" "I099s" "I241m" "I241s" "I418s" "I731m"
## [1016] "I731s" "I881m" "I881s" "J310m" "J310s" "J311m" "J311s"
## [1023] "J312m" "J312s" "J320m" "J320s" "J321m" "J321s" "J322m"
## [1030] "J322s" "J323m" "J323s" "J324m" "J324s" "J328m" "J328s"
## [1037] "J329m" "J329s" "J350m" "J350s" "J351m" "J351s" "J352m"
## [1044] "J352s" "J353m" "J358m" "J358s" "J359m" "J359s" "J370m"
## [1051] "J370s" "J40m" "J40s" "J410m" "J410s" "J411m" "J42m"
## [1058] "J42s" "J430m" "J430s" "J431m" "J431s" "J432m" "J432s"
## [1065] "J438m" "J438s" "J439m" "J439s" "J440m" "J440s" "J441m"
## [1072] "J441s" "J448m" "J448s" "J449m" "J449s" "J450m" "J450s"
## [1079] "J451m" "J451s" "J458m" "J458s" "J459m" "J459s" "J46m"
## [1086] "J46s" "J47m" "J47s" "J840m" "J840s" "J841m" "J841s"
## [1093] "J848m" "J848s" "J849m" "J849s" "K033m" "K033s" "K040m"
## [1100] "K040s" "K044m" "K044s" "K045m" "K045s" "K046m" "K046s"
## [1107] "K047m" "K047s" "K050m" "K050s" "K051m" "K051s" "K052m"
## [1114] "K052s" "K0522s" "K053m" "K053s" "K054m" "K054s" "K055m"
## [1121] "K055s" "K056m" "K056s" "K090m" "K090s" "K091m" "K091s"
## [1128] "K092m" "K092s" "K098m" "K098s" "K099m" "K099s" "K102m"
## [1135] "K102s" "K103m" "K103s" "K112m" "K112s" "K121m" "K121s"
## [1142] "K122m" "K122s" "K123m" "K123s" "K140m" "K140s" "K220m"
## [1149] "K220s" "K227m" "K227s" "K254m" "K254s" "K255m" "K255s"
## [1156] "K256m" "K256s" "K257m" "K257s" "K264m" "K264s" "K265m"
## [1163] "K265s" "K266m" "K266s" "K267m" "K267s" "K274m" "K274s"
## [1170] "K275m" "K275s" "K276m" "K276s" "K277m" "K277s" "K284m"
## [1177] "K285m" "K286m" "K287m" "K287s" "K292m" "K292s" "K293m"
## [1184] "K293s" "K294m" "K294s" "K295m" "K295s" "K296m" "K296s"
## [1191] "K500m" "K500s" "K501m" "K501s" "K508m" "K508s" "K509m"
## [1198] "K509s" "K510m" "K510s" "K511m" "K511s" "K512m" "K512s"
## [1205] "K513m" "K513s" "K514m" "K514s" "K515m" "K515s" "K518m"
## [1212] "K518s" "K519m" "K519s" "K520m" "K520s" "K521m" "K521s"
## [1219] "K522m" "K522s" "K523m" "K523s" "K528m" "K528s" "K529m"
## [1226] "K529s" "K580m" "K580s" "K589m" "K589s" "K601m" "K601s"
## [1233] "K700m" "K700s" "K701m" "K701s" "K702m" "K702s" "K703m"
## [1240] "K703s" "K704m" "K704s" "K709m" "K709s" "K710m" "K710s"
## [1247] "K711m" "K711s" "K712m" "K712s" "K713s" "K715m" "K716m"
## [1254] "K716s" "K717m" "K717s" "K718m" "K718s" "K719m" "K719s"
## [1261] "K720m" "K720s" "K721m" "K721s" "K729m" "K729s" "K730m"
## [1268] "K731m" "K731s" "K732m" "K732s" "K738m" "K738s" "K739m"
## [1275] "K739s" "K740m" "K740s" "K741m" "K741s" "K742m" "K742s"
## [1282] "K743m" "K743s" "K744m" "K744s" "K745m" "K745s" "K746m"
## [1289] "K746s" "K750m" "K750s" "K751s" "K752m" "K752s" "K753m"
## [1296] "K753s" "K754m" "K754s" "K758m" "K758s" "K759m" "K759s"
## [1303] "K760m" "K760s" "K761m" "K761s" "K762m" "K762s" "K763m"
## [1310] "K763s" "K765s" "K766m" "K766s" "K767m" "K767s" "K768m"
## [1317] "K768s" "K769m" "K769s" "K770m" "K770s" "K778s" "K811m"
## [1324] "K811s" "K830m" "K830s" "K860m" "K860s" "K861m" "K861s"
## [1331] "K900m" "K900s" "L410m" "L410s" "M300m" "M300s" "M301m"
## [1338] "M301s" "M302m" "M303m" "M303s" "M308m" "M308s" "M310m"
## [1345] "M310s" "M311m" "M311s" "M312s" "M313m" "M313s" "M314m"
## [1352] "M314s" "M315m" "M315s" "M316m" "M316s" "M317m" "M317s"
## [1359] "M318m" "M318s" "M319m" "M319s" "M320m" "M320s" "M321m"
## [1366] "M321s" "M328m" "M328s" "M329m" "M329s" "M3290m" "M3290s"
## [1373] "M330s" "M331m" "M331s" "M332m" "M332s" "M339m" "M339s"
## [1380] "M350m" "M350s" "M351m" "M351s" "M352m" "M352s" "M353m"
## [1387] "M353s" "M354m" "M354s" "M355s" "M357m" "M357s" "M358m"
## [1394] "M358s" "M359m" "M359s" "M3599s" "M360m" "M360s" "M362s"
## [1401] "M364s" "M368s" "M461m" "M461s" "M4616m" "M4616s" "M4617m"
## [1408] "M4617s" "M4618m" "M4618s" "M4619m" "M4619s" "M600m" "M600s"
## [1415] "M6000m" "M6000s" "M6001m" "M6001s" "M6002m" "M6005m" "M6005s"
## [1422] "M6006m" "M6006s" "M6008m" "M6008s" "M6009m" "M601s" "M6018s"
## [1429] "M602m" "M602s" "M6021s" "M6023m" "M6023s" "M6024m" "M6024s"
## [1436] "M6025m" "M6026s" "M6027m" "M6028m" "M6028s" "M6029s" "M608m"
## [1443] "M608s" "M6080m" "M6082m" "M6085m" "M6086s" "M6088m" "M6089m"
## [1450] "M6089s" "M609m" "M609s" "M6090m" "M6090s" "M6091m" "M6091s"
## [1457] "M6092m" "M6092s" "M6093m" "M6095m" "M6095s" "M6096m" "M6096s"
## [1464] "M6097m" "M6098m" "M6098s" "M6099m" "M6099s" "M610m" "M6106m"
## [1471] "M6114s" "M6115m" "M6125s" "M613s" "M614m" "M614s" "M615m"
## [1478] "M615s" "M6152m" "M6155m" "M6155s" "M6156m" "M6156s" "M6159m"
## [1485] "M619m" "M619s" "M6191s" "M6192s" "M6195m" "M6196s" "M6198s"
## [1492] "M632s" "M638s" "M863m" "M8630m" "N001m" "N001s" "N002s"
## [1499] "N004s" "N005m" "N007s" "N008m" "N008s" "N009m" "N009s"
## [1506] "N015s" "N017m" "N017s" "N019m" "N019s" "N030m" "N030s"
## [1513] "N031m" "N031s" "N032m" "N032s" "N033m" "N033s" "N035m"
## [1520] "N035s" "N036m" "N037m" "N037s" "N038m" "N038s" "N039m"
## [1527] "N039s" "N050m" "N050s" "N051m" "N051s" "N052m" "N052s"
## [1534] "N053m" "N053s" "N054m" "N055m" "N055s" "N056m" "N056s"
## [1541] "N057m" "N057s" "N058m" "N058s" "N059m" "N059s" "N301m"
## [1548] "N301s" "N411m" "N411s" "N701m" "N701s" "N711m" "N711s"
## [1555] "N731m" "N731s" "N734s" "N761m" "N761s"Create summary column
autoinflammatory_no_duplicate$ICD.autoinflammatory.raw <-
apply(
autoinflammatory_no_duplicate[,2:ncol(autoinflammatory_no_duplicate)] == 1,
1,
any)
autoinflammatory_no_duplicate$ICD.autoinflammatory <-
as.integer(
autoinflammatory_no_duplicate$ICD.autoinflammatory.raw
)
autoinflammatory_reduced <- autoinflammatory_no_duplicate %>%
select(IID, ICD.autoinflammatory)Summary
summary(as.factor(autoinflammatory_reduced$ICD.autoinflammatory))## 0 1
## 352522 150097Read in data
immunodeficiency <- fread(
input = "data_raw/2019_05_29_ICD/ICD10.immunodeficiency.txt",
header = TRUE,
stringsAsFactors = F,
data.table = F)
colnames(immunodeficiency)## [1] "IID" "B200m" "IID" "B201m" "IID" "B202m" "B202s" "IID"
## [9] "B203m" "B203s" "IID" "B204m" "B204s" "IID" "B206m" "B206s"
## [17] "IID" "B207m" "B207s" "IID" "B208m" "B208s" "IID" "B210m"
## [25] "B210s" "IID" "B211m" "IID" "B212m" "B212s" "IID" "B213m"
## [33] "B213s" "IID" "B217m" "IID" "B218m" "IID" "B220m" "B220s"
## [41] "IID" "B221m" "B221s" "IID" "B222m" "IID" "B227m" "B227s"
## [49] "IID" "B230m" "B230s" "IID" "B232m" "B232s" "IID" "B238m"
## [57] "B238s" "IID" "B24m" "B24s" "IID" "D71m" "D71s" "IID"
## [65] "D760m" "D760s" "IID" "D761m" "D761s" "IID" "D762s" "IID"
## [73] "D763m" "D763s" "IID" "D800m" "D800s" "IID" "D801m" "D801s"
## [81] "IID" "D802m" "D802s" "IID" "D803m" "D803s" "IID" "D804m"
## [89] "D804s" "IID" "D805m" "D805s" "IID" "D806m" "D806s" "IID"
## [97] "D808m" "D808s" "IID" "D809m" "D809s" "IID" "D810m" "IID"
## [105] "D811m" "D811s" "IID" "D818m" "IID" "D819m" "D819s" "IID"
## [113] "D821m" "D821s" "IID" "D823m" "D823s" "IID" "D824m" "D824s"
## [121] "IID" "D829m" "D829s" "IID" "D830m" "D830s" "IID" "D831m"
## [129] "D831s" "IID" "D832m" "IID" "D838m" "D838s" "IID" "D839m"
## [137] "D839s" "IID" "D840s" "IID" "D841m" "D841s" "IID" "D848m"
## [145] "D848s" "IID" "D849m" "D849s"Remove duplicate column
immunodeficiency_no_duplicate <- immunodeficiency[!duplicated(as.list(immunodeficiency))]
colnames(immunodeficiency_no_duplicate)## [1] "IID" "B200m" "B201m" "B202m" "B202s" "B203m" "B203s" "B204m"
## [9] "B204s" "B206m" "B206s" "B207m" "B207s" "B208m" "B208s" "B210m"
## [17] "B210s" "B211m" "B212m" "B212s" "B213m" "B213s" "B217m" "B218m"
## [25] "B220m" "B220s" "B221m" "B221s" "B222m" "B227m" "B227s" "B230m"
## [33] "B230s" "B232m" "B232s" "B238m" "B238s" "B24m" "B24s" "D71m"
## [41] "D71s" "D760m" "D760s" "D761m" "D761s" "D762s" "D763m" "D763s"
## [49] "D800m" "D800s" "D801m" "D801s" "D802m" "D802s" "D803m" "D803s"
## [57] "D804m" "D804s" "D805m" "D805s" "D806m" "D806s" "D808m" "D808s"
## [65] "D809m" "D809s" "D810m" "D811m" "D819m" "D819s" "D821m" "D821s"
## [73] "D823m" "D823s" "D824m" "D829m" "D829s" "D830m" "D830s" "D831m"
## [81] "D831s" "D838m" "D838s" "D839m" "D839s" "D840s" "D841m" "D841s"
## [89] "D848m" "D848s" "D849m" "D849s"Create summary column
immunodeficiency_no_duplicate$ICD.immunodeficiency.raw <-
apply(
immunodeficiency_no_duplicate[,2:ncol(immunodeficiency_no_duplicate)] == 1,
1,
any)
immunodeficiency_no_duplicate$ICD.immunodeficiency <-
as.integer(
immunodeficiency_no_duplicate$ICD.immunodeficiency.raw
)
immunodeficiency_reduced <- immunodeficiency_no_duplicate %>%
select(IID, ICD.immunodeficiency)Summary
summary(as.factor(immunodeficiency_reduced$ICD.immunodeficiency))## 0 1
## 502050 569Read in data
memory <- fread(
input = "data_raw/2019_05_29_ICD/ICD10.memory.txt",
header = TRUE,
stringsAsFactors = F,
data.table = F)
colnames(memory)## [1] "IID" "F000m" "F000s" "IID" "F001m" "F001s" "IID" "F002m"
## [9] "F002s" "IID" "F009m" "F009s" "IID" "F010m" "F010s" "IID"
## [17] "F011m" "F011s" "IID" "F012s" "IID" "F013m" "IID" "F019m"
## [25] "F019s" "IID" "F020m" "F020s" "IID" "F023m" "F023s" "IID"
## [33] "F024s" "IID" "F028m" "F028s" "IID" "F03m" "F03s" "IID"
## [41] "F04s" "IID" "F050m" "F050s" "IID" "F051m" "F051s" "IID"
## [49] "F058m" "F058s" "IID" "F059m" "F059s" "IID" "F06m" "IID"
## [57] "F060m" "F060s" "IID" "F062m" "F062s" "IID" "F063m" "F063s"
## [65] "IID" "F064m" "F064s" "IID" "F066s" "IID" "F067m" "F067s"
## [73] "IID" "F068m" "F068s" "IID" "F069m" "F069s" "IID" "F070m"
## [81] "F070s" "IID" "F071m" "F071s" "IID" "F072m" "F072s" "IID"
## [89] "F078m" "F078s" "IID" "F079m" "F079s" "IID" "F09m" "F09s"
## [97] "IID" "G10m" "G10s" "IID" "G20m" "G20s" "IID" "G210m"
## [105] "G210s" "IID" "G211m" "G211s" "IID" "G212s" "IID" "G213s"
## [113] "IID" "G214m" "G214s" "IID" "G218m" "G218s" "IID" "G219m"
## [121] "G219s" "IID" "G231m" "G231s" "IID" "G238m" "G238s" "IID"
## [129] "G239s" "IID" "G240m" "G240s" "IID" "G241m" "G241s" "IID"
## [137] "G242s" "IID" "G243m" "G243s" "IID" "G244m" "G244s" "IID"
## [145] "G245m" "G245s" "IID" "G248m" "G248s" "IID" "G249m" "G249s"
## [153] "IID" "G250m" "G250s" "IID" "G251m" "G251s" "IID" "G252m"
## [161] "G252s" "IID" "G253m" "G253s" "IID" "G255m" "G255s" "IID"
## [169] "G258m" "G258s" "IID" "G259m" "G259s" "IID" "G300m" "G300s"
## [177] "IID" "G301m" "G301s" "IID" "G308m" "G308s" "IID" "G309m"
## [185] "G309s" "IID" "G310m" "G310s" "IID" "G311s" "IID" "G312m"
## [193] "G312s" "IID" "G318m" "G318s" "IID" "G319m" "G319s" "IID"
## [201] "G320m" "G320s" "IID" "G328m" "G328s"Remove duplicate column
memory_no_duplicate <- memory[!duplicated(as.list(memory))]
colnames(memory_no_duplicate)## [1] "IID" "F000m" "F000s" "F001m" "F001s" "F002m" "F002s" "F009m"
## [9] "F009s" "F010m" "F010s" "F011m" "F011s" "F012s" "F013m" "F019m"
## [17] "F019s" "F020m" "F020s" "F023m" "F023s" "F024s" "F028m" "F028s"
## [25] "F03m" "F03s" "F04s" "F050m" "F050s" "F051m" "F051s" "F058m"
## [33] "F058s" "F059m" "F059s" "F06m" "F060m" "F060s" "F062m" "F062s"
## [41] "F063m" "F063s" "F064m" "F064s" "F066s" "F067m" "F067s" "F068m"
## [49] "F068s" "F069m" "F069s" "F070m" "F070s" "F071m" "F071s" "F072m"
## [57] "F072s" "F078m" "F078s" "F079m" "F079s" "F09m" "F09s" "G10m"
## [65] "G10s" "G20m" "G20s" "G210m" "G210s" "G211m" "G211s" "G212s"
## [73] "G213s" "G214m" "G214s" "G218m" "G218s" "G219m" "G219s" "G231m"
## [81] "G231s" "G238m" "G238s" "G239s" "G240m" "G240s" "G241m" "G241s"
## [89] "G242s" "G243m" "G243s" "G244m" "G244s" "G245m" "G245s" "G248m"
## [97] "G248s" "G249m" "G249s" "G250m" "G250s" "G251m" "G251s" "G252m"
## [105] "G252s" "G253m" "G253s" "G255m" "G255s" "G258m" "G258s" "G259m"
## [113] "G259s" "G300m" "G300s" "G301m" "G301s" "G308m" "G308s" "G309m"
## [121] "G309s" "G310m" "G310s" "G311s" "G312m" "G312s" "G318m" "G318s"
## [129] "G319m" "G319s" "G320m" "G320s" "G328m" "G328s"Create summary column
memory_no_duplicate$ICD.memory.raw <-
apply(
memory_no_duplicate[,2:ncol(memory_no_duplicate)] == 1,
1,
any)
memory_no_duplicate$ICD.memory <-
as.integer(
memory_no_duplicate$ICD.memory.raw
)
memory_reduced <- memory_no_duplicate %>%
select(IID, ICD.memory)Summary
summary(as.factor(memory_reduced$ICD.memory))## 0 1
## 497863 4756Read in data
metabolic <- fread(
input = "data_raw/2019_05_29_ICD/ICD10.metabolic.txt",
header = TRUE,
stringsAsFactors = F,
data.table = F)
colnames(metabolic)## [1] "IID" "E011m" "E011s" "IID" "E018s" "IID" "E02m" "E02s"
## [9] "IID" "E030m" "E030s" "IID" "E031s" "IID" "E032m" "E032s"
## [17] "IID" "E033s" "IID" "E034m" "IID" "E035s" "IID" "E038m"
## [25] "E038s" "IID" "E039m" "E039s" "IID" "E040m" "E040s" "IID"
## [33] "E041m" "E041s" "IID" "E042m" "E042s" "IID" "E048m" "E048s"
## [41] "IID" "E049m" "E049s" "IID" "E05s" "IID" "E050m" "E050s"
## [49] "IID" "E051m" "E051s" "IID" "E052m" "E052s" "IID" "E053m"
## [57] "E053s" "IID" "E054s" "IID" "E055m" "E055s" "IID" "E058m"
## [65] "E058s" "IID" "E059m" "E059s" "IID" "E060m" "IID" "E061m"
## [73] "E061s" "IID" "E062m" "E062s" "IID" "E063m" "E063s" "IID"
## [81] "E064m" "E064s" "IID" "E065m" "E065s" "IID" "E069m" "E069s"
## [89] "IID" "E070m" "E070s" "IID" "E071s" "IID" "E078m" "E078s"
## [97] "IID" "E079m" "E079s" "IID" "E100m" "E100s" "IID" "E101m"
## [105] "E101s" "IID" "E102m" "E102s" "IID" "E103m" "E103s" "IID"
## [113] "E104m" "E104s" "IID" "E105m" "E105s" "IID" "E106m" "E106s"
## [121] "IID" "E107m" "E107s" "IID" "E108m" "E108s" "IID" "E109m"
## [129] "E109s" "IID" "E110m" "E110s" "IID" "E111m" "E111s" "IID"
## [137] "E112m" "E112s" "IID" "E113m" "E113s" "IID" "E114m" "E114s"
## [145] "IID" "E115m" "E115s" "IID" "E116m" "E116s" "IID" "E117m"
## [153] "E117s" "IID" "E118m" "E118s" "IID" "E119m" "E119s" "IID"
## [161] "E121s" "IID" "E128s" "IID" "E129s" "IID" "E131m" "E131s"
## [169] "IID" "E132s" "IID" "E133m" "E133s" "IID" "E135s" "IID"
## [177] "E136s" "IID" "E137s" "IID" "E138m" "E138s" "IID" "E139m"
## [185] "E139s" "IID" "E140m" "E140s" "IID" "E141m" "E141s" "IID"
## [193] "E142m" "E142s" "IID" "E143m" "E143s" "IID" "E144m" "E144s"
## [201] "IID" "E145m" "E145s" "IID" "E146m" "E146s" "IID" "E147m"
## [209] "E147s" "IID" "E148m" "E148s" "IID" "E149m" "E149s" "IID"
## [217] "E15m" "E15s" "IID" "E160m" "E160s" "IID" "E161m" "E161s"
## [225] "IID" "E162m" "E162s" "IID" "E163s" "IID" "E164m" "E164s"
## [233] "IID" "E168s" "IID" "E169m" "E169s" "IID" "E201m" "E201s"
## [241] "IID" "E208s" "IID" "E209m" "E209s" "IID" "E210m" "E210s"
## [249] "IID" "E211m" "E211s" "IID" "E212m" "E212s" "IID" "E213m"
## [257] "E213s" "IID" "E214m" "E214s" "IID" "E215m" "E215s" "IID"
## [265] "E220m" "E220s" "IID" "E221m" "E221s" "IID" "E222m" "E222s"
## [273] "IID" "E228m" "E228s" "IID" "E229m" "E229s" "IID" "E230m"
## [281] "E230s" "IID" "E231m" "E231s" "IID" "E232m" "E232s" "IID"
## [289] "E233m" "E233s" "IID" "E236m" "E236s" "IID" "E237m" "E237s"
## [297] "IID" "E240m" "E240s" "IID" "E241m" "E241s" "IID" "E242m"
## [305] "E242s" "IID" "E243s" "IID" "E248m" "E248s" "IID" "E249m"
## [313] "E249s" "IID" "E250m" "E250s" "IID" "E258m" "IID" "E259m"
## [321] "E259s" "IID" "E260m" "E260s" "IID" "E261s" "IID" "E268s"
## [329] "IID" "E269m" "E269s" "IID" "E270s" "IID" "E271m" "E271s"
## [337] "IID" "E272m" "E272s" "IID" "E273m" "E273s" "IID" "E274m"
## [345] "E274s" "IID" "E275m" "E275s" "IID" "E278m" "E278s" "IID"
## [353] "E279m" "E279s" "IID" "E281m" "IID" "E282m" "E282s" "IID"
## [361] "E283m" "E283s" "IID" "E288m" "E288s" "IID" "E289m" "IID"
## [369] "E290m" "E290s" "IID" "E291m" "E291s" "IID" "E298m" "E298s"
## [377] "IID" "E299m" "E299s" "IID" "E300s" "IID" "E309s" "IID"
## [385] "E310m" "E310s" "IID" "E318m" "IID" "E319s" "IID" "E320m"
## [393] "E320s" "IID" "E328m" "E328s" "IID" "E329m" "E329s" "IID"
## [401] "E340m" "E340s" "IID" "E343s" "IID" "E345m" "E345s" "IID"
## [409] "E348m" "E348s" "IID" "E349m" "E349s" "IID" "E351s" "IID"
## [417] "E700s" "IID" "E701s" "IID" "E702m" "E702s" "IID" "E703m"
## [425] "E703s" "IID" "E708s" "IID" "E709s" "IID" "E711m" "E711s"
## [433] "IID" "E713m" "E713s" "IID" "E720m" "E720s" "IID" "E721m"
## [441] "E721s" "IID" "E722m" "E722s" "IID" "E724s" "IID" "E725m"
## [449] "E725s" "IID" "E731m" "IID" "E738s" "IID" "E739m" "E739s"
## [457] "IID" "E740m" "E740s" "IID" "E742s" "IID" "E743m" "E743s"
## [465] "IID" "E744s" "IID" "E748s" "IID" "E749m" "IID" "E750s"
## [473] "IID" "E752m" "E752s" "IID" "E753s" "IID" "E754s" "IID"
## [481] "E755m" "E755s" "IID" "E756s" "IID" "E760s" "IID" "E761s"
## [489] "IID" "E762m" "E762s" "IID" "E778m" "E778s" "IID" "E780m"
## [497] "E780s" "IID" "E781m" "E781s" "IID" "E782m" "E782s" "IID"
## [505] "E783s" "IID" "E784m" "E784s" "IID" "E785m" "E785s" "IID"
## [513] "E786s" "IID" "E788s" "IID" "E789m" "E789s" "IID" "E790s"
## [521] "IID" "E791s" "IID" "E798s" "IID" "E800s" "IID" "E801m"
## [529] "E801s" "IID" "E802m" "E802s" "IID" "E804m" "E804s" "IID"
## [537] "E806m" "E806s" "IID" "E807s" "IID" "E830m" "E830s" "IID"
## [545] "E831m" "E831s" "IID" "E832m" "E832s" "IID" "E833m" "E833s"
## [553] "IID" "E834m" "E834s" "IID" "E835m" "E835s" "IID" "E838s"
## [561] "IID" "E839m" "E839s" "IID" "E840m" "E840s" "IID" "E841m"
## [569] "E841s" "IID" "E848m" "E848s" "IID" "E849m" "E849s" "IID"
## [577] "E850m" "E850s" "IID" "E851m" "E851s" "IID" "E852s" "IID"
## [585] "E853m" "E853s" "IID" "E854m" "E854s" "IID" "E858m" "E858s"
## [593] "IID" "E859m" "E859s" "IID" "E86m" "E86s" "IID" "E870m"
## [601] "E870s" "IID" "E871m" "E871s" "IID" "E872m" "E872s" "IID"
## [609] "E873m" "E873s" "IID" "E874s" "IID" "E875m" "E875s" "IID"
## [617] "E876m" "E876s" "IID" "E877m" "E877s" "IID" "E878m" "E878s"
## [625] "IID" "E880m" "E880s" "IID" "E881m" "E881s" "IID" "E882m"
## [633] "E882s" "IID" "E883m" "E883s" "IID" "E888m" "E888s" "IID"
## [641] "E889m" "E889s" "IID" "E890m" "E890s" "IID" "E891m" "E891s"
## [649] "IID" "E892m" "E892s" "IID" "E893m" "E893s" "IID" "E894m"
## [657] "E894s" "IID" "E895m" "E895s" "IID" "E896m" "E896s" "IID"
## [665] "E898m" "E898s" "IID" "E899m" "E899s"Remove duplicate column
metabolic_no_duplicate <- metabolic[!duplicated(as.list(metabolic))]
colnames(metabolic_no_duplicate)## [1] "IID" "E011m" "E011s" "E018s" "E02m" "E02s" "E030m" "E030s"
## [9] "E031s" "E032m" "E032s" "E033s" "E034m" "E035s" "E038m" "E038s"
## [17] "E039m" "E039s" "E040m" "E040s" "E041m" "E041s" "E042m" "E042s"
## [25] "E048m" "E048s" "E049m" "E049s" "E05s" "E050m" "E050s" "E051m"
## [33] "E051s" "E052m" "E052s" "E053m" "E053s" "E054s" "E055m" "E055s"
## [41] "E058m" "E058s" "E059m" "E059s" "E060m" "E061m" "E061s" "E062m"
## [49] "E062s" "E063m" "E063s" "E064m" "E064s" "E065m" "E065s" "E069m"
## [57] "E069s" "E070m" "E070s" "E071s" "E078m" "E078s" "E079m" "E079s"
## [65] "E100m" "E100s" "E101m" "E101s" "E102m" "E102s" "E103m" "E103s"
## [73] "E104m" "E104s" "E105m" "E105s" "E106m" "E106s" "E107m" "E107s"
## [81] "E108m" "E108s" "E109m" "E109s" "E110m" "E110s" "E111m" "E111s"
## [89] "E112m" "E112s" "E113m" "E113s" "E114m" "E114s" "E115m" "E115s"
## [97] "E116m" "E116s" "E117m" "E117s" "E118m" "E118s" "E119m" "E119s"
## [105] "E121s" "E128s" "E129s" "E131m" "E131s" "E132s" "E133m" "E133s"
## [113] "E135s" "E136s" "E137s" "E138m" "E138s" "E139m" "E139s" "E140m"
## [121] "E140s" "E141m" "E141s" "E142m" "E142s" "E143m" "E143s" "E144m"
## [129] "E144s" "E145m" "E145s" "E146m" "E146s" "E147m" "E147s" "E148m"
## [137] "E148s" "E149m" "E149s" "E15m" "E15s" "E160m" "E160s" "E161m"
## [145] "E161s" "E162m" "E162s" "E163s" "E164m" "E164s" "E168s" "E169m"
## [153] "E169s" "E201m" "E201s" "E208s" "E209m" "E209s" "E210m" "E210s"
## [161] "E211m" "E211s" "E212m" "E212s" "E213m" "E213s" "E214m" "E214s"
## [169] "E215m" "E215s" "E220m" "E220s" "E221m" "E221s" "E222m" "E222s"
## [177] "E228m" "E228s" "E229m" "E229s" "E230m" "E230s" "E231m" "E231s"
## [185] "E232m" "E232s" "E233m" "E233s" "E236m" "E236s" "E237m" "E237s"
## [193] "E240m" "E240s" "E241m" "E241s" "E242m" "E242s" "E243s" "E248m"
## [201] "E248s" "E249m" "E249s" "E250m" "E250s" "E258m" "E259m" "E259s"
## [209] "E260m" "E260s" "E261s" "E268s" "E269m" "E269s" "E270s" "E271m"
## [217] "E271s" "E272m" "E272s" "E273m" "E273s" "E274m" "E274s" "E275m"
## [225] "E275s" "E278m" "E278s" "E279m" "E279s" "E281m" "E282m" "E282s"
## [233] "E283m" "E283s" "E288m" "E288s" "E289m" "E290m" "E290s" "E291m"
## [241] "E291s" "E298m" "E298s" "E299m" "E299s" "E300s" "E309s" "E310m"
## [249] "E310s" "E318m" "E319s" "E320m" "E320s" "E328m" "E328s" "E329m"
## [257] "E329s" "E340m" "E340s" "E343s" "E345m" "E345s" "E348m" "E348s"
## [265] "E349m" "E349s" "E351s" "E700s" "E701s" "E702m" "E702s" "E703m"
## [273] "E703s" "E708s" "E709s" "E711m" "E711s" "E713m" "E713s" "E720m"
## [281] "E720s" "E721m" "E721s" "E722m" "E722s" "E724s" "E725m" "E725s"
## [289] "E731m" "E738s" "E739m" "E739s" "E740m" "E740s" "E742s" "E743m"
## [297] "E743s" "E744s" "E748s" "E749m" "E750s" "E752m" "E752s" "E753s"
## [305] "E754s" "E755m" "E755s" "E756s" "E760s" "E761s" "E762m" "E762s"
## [313] "E778m" "E778s" "E780m" "E780s" "E781m" "E781s" "E782m" "E782s"
## [321] "E783s" "E784m" "E784s" "E785m" "E785s" "E786s" "E788s" "E789m"
## [329] "E789s" "E790s" "E791s" "E798s" "E800s" "E801m" "E801s" "E802m"
## [337] "E802s" "E804m" "E804s" "E806m" "E806s" "E807s" "E830m" "E830s"
## [345] "E831m" "E831s" "E832m" "E832s" "E833m" "E833s" "E834m" "E834s"
## [353] "E835m" "E835s" "E838s" "E839m" "E839s" "E840m" "E840s" "E841m"
## [361] "E841s" "E848m" "E848s" "E849m" "E849s" "E850m" "E850s" "E851m"
## [369] "E851s" "E852s" "E853m" "E853s" "E854m" "E854s" "E858m" "E858s"
## [377] "E859m" "E859s" "E86m" "E86s" "E870m" "E870s" "E871m" "E871s"
## [385] "E872m" "E872s" "E873m" "E873s" "E874s" "E875m" "E875s" "E876m"
## [393] "E876s" "E877m" "E877s" "E878m" "E878s" "E880m" "E880s" "E881m"
## [401] "E881s" "E882m" "E882s" "E883m" "E883s" "E888m" "E888s" "E889m"
## [409] "E889s" "E890m" "E890s" "E891m" "E891s" "E892m" "E892s" "E893m"
## [417] "E893s" "E894m" "E894s" "E895m" "E895s" "E896m" "E896s" "E898m"
## [425] "E898s" "E899m" "E899s"Create summary column
metabolic_no_duplicate$ICD.metabolic.raw <-
apply(
metabolic_no_duplicate[,2:ncol(metabolic_no_duplicate)] == 1,
1,
any)
metabolic_no_duplicate$ICD.metabolic <-
as.integer(
metabolic_no_duplicate$ICD.metabolic.raw
)
metabolic_reduced <- metabolic_no_duplicate %>%
select(IID, ICD.metabolic)Summary
summary(as.factor(metabolic_reduced$ICD.metabolic))## 0 1
## 418254 84365Read in data
psychiatric <- fread(
input = "data_raw/2019_05_29_ICD/ICD10.psychiatric.txt",
header = TRUE,
stringsAsFactors = F,
data.table = F)
colnames(psychiatric)## [1] "IID" "F000m" "F000s" "IID" "F001m" "F001s" "IID" "F002m"
## [9] "F002s" "IID" "F009m" "F009s" "IID" "F010m" "F010s" "IID"
## [17] "F011m" "F011s" "IID" "F012s" "IID" "F013m" "IID" "F019m"
## [25] "F019s" "IID" "F020m" "F020s" "IID" "F023m" "F023s" "IID"
## [33] "F024s" "IID" "F028m" "F028s" "IID" "F03m" "F03s" "IID"
## [41] "F04s" "IID" "F050m" "F050s" "IID" "F051m" "F051s" "IID"
## [49] "F058m" "F058s" "IID" "F059m" "F059s" "IID" "F06m" "IID"
## [57] "F060m" "F060s" "IID" "F062m" "F062s" "IID" "F063m" "F063s"
## [65] "IID" "F064m" "F064s" "IID" "F066s" "IID" "F067m" "F067s"
## [73] "IID" "F068m" "F068s" "IID" "F069m" "F069s" "IID" "F070m"
## [81] "F070s" "IID" "F071m" "F071s" "IID" "F072m" "F072s" "IID"
## [89] "F078m" "F078s" "IID" "F079m" "F079s" "IID" "F09m" "F09s"
## [97] "IID" "F10m" "F10s" "IID" "F100m" "F100s" "IID" "F101m"
## [105] "F101s" "IID" "F102m" "F102s" "IID" "F103m" "F103s" "IID"
## [113] "F104m" "F104s" "IID" "F105m" "F105s" "IID" "F106m" "F106s"
## [121] "IID" "F107m" "F107s" "IID" "F108m" "F108s" "IID" "F109m"
## [129] "F109s" "IID" "F110m" "F110s" "IID" "F111s" "IID" "F112m"
## [137] "F112s" "IID" "F113m" "F113s" "IID" "F114m" "IID" "F115m"
## [145] "F115s" "IID" "F117m" "IID" "F119s" "IID" "F120m" "F120s"
## [153] "IID" "F121m" "F121s" "IID" "F122m" "F122s" "IID" "F125m"
## [161] "IID" "F128s" "IID" "F129s" "IID" "F130s" "IID" "F131s"
## [169] "IID" "F132m" "F132s" "IID" "F133m" "F133s" "IID" "F134s"
## [177] "IID" "F139s" "IID" "F140s" "IID" "F141m" "F141s" "IID"
## [185] "F142m" "F142s" "IID" "F145s" "IID" "F149s" "IID" "F150m"
## [193] "F150s" "IID" "F151m" "F151s" "IID" "F152s" "IID" "F153s"
## [201] "IID" "F155m" "IID" "F158s" "IID" "F159s" "IID" "F161s"
## [209] "IID" "F162m" "F162s" "IID" "F163m" "IID" "F165m" "IID"
## [217] "F168s" "IID" "F169m" "IID" "F170m" "F170s" "IID" "F171m"
## [225] "F171s" "IID" "F172m" "F172s" "IID" "F173m" "F173s" "IID"
## [233] "F174s" "IID" "F179s" "IID" "F181s" "IID" "F182s" "IID"
## [241] "F185m" "IID" "F189s" "IID" "F190s" "IID" "F191m" "F191s"
## [249] "IID" "F192m" "F192s" "IID" "F193m" "F193s" "IID" "F194s"
## [257] "IID" "F195m" "F195s" "IID" "F198m" "F198s" "IID" "F199m"
## [265] "F199s" "IID" "F20m" "F20s" "IID" "F200m" "F200s" "IID"
## [273] "F201m" "IID" "F202m" "F202s" "IID" "F203m" "IID" "F204m"
## [281] "F204s" "IID" "F205m" "F205s" "IID" "F206m" "F206s" "IID"
## [289] "F208m" "F208s" "IID" "F209m" "F209s" "IID" "F21m" "F21s"
## [297] "IID" "F220m" "F220s" "IID" "F228m" "F228s" "IID" "F229m"
## [305] "F229s" "IID" "F23s" "IID" "F230m" "F230s" "IID" "F231m"
## [313] "F231s" "IID" "F232m" "IID" "F233m" "F233s" "IID" "F238m"
## [321] "IID" "F239m" "F239s" "IID" "F24m" "IID" "F250m" "F250s"
## [329] "IID" "F251m" "F251s" "IID" "F252m" "F252s" "IID" "F258m"
## [337] "F258s" "IID" "F259m" "F259s" "IID" "F28m" "F28s" "IID"
## [345] "F29m" "F29s" "IID" "F300m" "F300s" "IID" "F301m" "F301s"
## [353] "IID" "F302m" "F302s" "IID" "F308m" "F308s" "IID" "F309m"
## [361] "F309s" "IID" "F310m" "F310s" "IID" "F311m" "F311s" "IID"
## [369] "F312m" "F312s" "IID" "F313m" "F313s" "IID" "F314m" "F314s"
## [377] "IID" "F315m" "F315s" "IID" "F316m" "F316s" "IID" "F317m"
## [385] "F317s" "IID" "F318m" "F318s" "IID" "F319m" "F319s" "IID"
## [393] "F32m" "IID" "F320m" "F320s" "IID" "F321m" "F321s" "IID"
## [401] "F322m" "F322s" "IID" "F323m" "F323s" "IID" "F328m" "F328s"
## [409] "IID" "F329m" "F329s" "IID" "F330m" "F330s" "IID" "F331m"
## [417] "F331s" "IID" "F332m" "F332s" "IID" "F333m" "F333s" "IID"
## [425] "F334m" "F334s" "IID" "F338m" "F338s" "IID" "F339m" "F339s"
## [433] "IID" "F340m" "F340s" "IID" "F341m" "F341s" "IID" "F348m"
## [441] "F348s" "IID" "F349s" "IID" "F380m" "F380s" "IID" "F381s"
## [449] "IID" "F388m" "F388s" "IID" "F39m" "F39s" "IID" "F400m"
## [457] "F400s" "IID" "F401m" "F401s" "IID" "F402m" "F402s" "IID"
## [465] "F408m" "F408s" "IID" "F409s" "IID" "F410m" "F410s" "IID"
## [473] "F411m" "F411s" "IID" "F412m" "F412s" "IID" "F413m" "F413s"
## [481] "IID" "F418m" "F418s" "IID" "F419m" "F419s" "IID" "F420m"
## [489] "F420s" "IID" "F421m" "F421s" "IID" "F422m" "F422s" "IID"
## [497] "F428m" "F428s" "IID" "F429m" "F429s" "IID" "F430m" "F430s"
## [505] "IID" "F431m" "F431s" "IID" "F432m" "F432s" "IID" "F438m"
## [513] "F438s" "IID" "F439m" "F439s" "IID" "F440m" "F440s" "IID"
## [521] "F441m" "F441s" "IID" "F443m" "F443s" "IID" "F444m" "F444s"
## [529] "IID" "F445m" "F445s" "IID" "F446m" "F446s" "IID" "F447m"
## [537] "IID" "F448m" "F448s" "IID" "F449m" "F449s" "IID" "F450m"
## [545] "F450s" "IID" "F451s" "IID" "F452m" "F452s" "IID" "F453m"
## [553] "F453s" "IID" "F454m" "F454s" "IID" "F458m" "F458s" "IID"
## [561] "F459m" "F459s" "IID" "F480m" "F480s" "IID" "F481s" "IID"
## [569] "F488m" "F488s" "IID" "F489m" "F489s" "IID" "F500m" "F500s"
## [577] "IID" "F501m" "F501s" "IID" "F502m" "F502s" "IID" "F505m"
## [585] "F505s" "IID" "F508m" "F508s" "IID" "F509m" "F509s" "IID"
## [593] "F510m" "F510s" "IID" "F511m" "F511s" "IID" "F512s" "IID"
## [601] "F513m" "F513s" "IID" "F514m" "F514s" "IID" "F515m" "F515s"
## [609] "IID" "F519m" "F519s" "IID" "F520m" "F520s" "IID" "F521s"
## [617] "IID" "F522m" "F522s" "IID" "F524m" "F524s" "IID" "F526m"
## [625] "F526s" "IID" "F527m" "F527s" "IID" "F528m" "IID" "F529m"
## [633] "F529s" "IID" "F530m" "F530s" "IID" "F531m" "F531s" "IID"
## [641] "F538s" "IID" "F539m" "IID" "F54m" "F54s" "IID" "F55s"
## [649] "IID" "F59m" "F59s" "IID" "F600m" "F600s" "IID" "F601m"
## [657] "F601s" "IID" "F602m" "F602s" "IID" "F603m" "F603s" "IID"
## [665] "F604m" "F604s" "IID" "F605m" "F605s" "IID" "F606m" "F606s"
## [673] "IID" "F607m" "F607s" "IID" "F608m" "F608s" "IID" "F609m"
## [681] "F609s" "IID" "F61m" "F61s" "IID" "F620m" "F620s" "IID"
## [689] "F621m" "F621s" "IID" "F628m" "F628s" "IID" "F629m" "F629s"
## [697] "IID" "F630m" "F630s" "IID" "F631s" "IID" "F633m" "F633s"
## [705] "IID" "F638s" "IID" "F639s" "IID" "F640m" "F640s" "IID"
## [713] "F641s" "IID" "F648m" "IID" "F649s" "IID" "F650s" "IID"
## [721] "F659s" "IID" "F660s" "IID" "F661s" "IID" "F662s" "IID"
## [729] "F669s" "IID" "F680s" "IID" "F681m" "F681s" "IID" "F69m"
## [737] "F69s" "IID" "F700m" "F700s" "IID" "F701m" "IID" "F708m"
## [745] "IID" "F709m" "F709s" "IID" "F711s" "IID" "F719s" "IID"
## [753] "F729s" "IID" "F789m" "F789s" "IID" "F790s" "IID" "F799s"
## [761] "IID" "F800m" "F800s" "IID" "F801m" "F801s" "IID" "F802m"
## [769] "F802s" "IID" "F803s" "IID" "F809s" "IID" "F810m" "F810s"
## [777] "IID" "F812s" "IID" "F819m" "F819s" "IID" "F82m" "F82s"
## [785] "IID" "F840s" "IID" "F841m" "F841s" "IID" "F843s" "IID"
## [793] "F845m" "F845s" "IID" "F89s" "IID" "F900s" "IID" "F911s"
## [801] "IID" "F918m" "F918s" "IID" "F919m" "F919s" "IID" "F920s"
## [809] "IID" "F929s" "IID" "F940s" "IID" "F950s" "IID" "F951m"
## [817] "F951s" "IID" "F952m" "F952s" "IID" "F959s" "IID" "F981m"
## [825] "IID" "F985m" "F985s" "IID" "F988s" "IID" "F99m" "F99s"Remove duplicate column
psychiatric_no_duplicate <- psychiatric[!duplicated(as.list(psychiatric))]
colnames(psychiatric_no_duplicate)## [1] "IID" "F000m" "F000s" "F001m" "F001s" "F002m" "F002s" "F009m"
## [9] "F009s" "F010m" "F010s" "F011m" "F011s" "F012s" "F013m" "F019m"
## [17] "F019s" "F020m" "F020s" "F023m" "F023s" "F024s" "F028m" "F028s"
## [25] "F03m" "F03s" "F04s" "F050m" "F050s" "F051m" "F051s" "F058m"
## [33] "F058s" "F059m" "F059s" "F06m" "F060m" "F060s" "F062m" "F062s"
## [41] "F063m" "F063s" "F064m" "F064s" "F066s" "F067m" "F067s" "F068m"
## [49] "F068s" "F069m" "F069s" "F070m" "F070s" "F071m" "F071s" "F072m"
## [57] "F072s" "F078m" "F078s" "F079m" "F079s" "F09m" "F09s" "F10m"
## [65] "F10s" "F100m" "F100s" "F101m" "F101s" "F102m" "F102s" "F103m"
## [73] "F103s" "F104m" "F104s" "F105m" "F105s" "F106m" "F106s" "F107m"
## [81] "F107s" "F108m" "F108s" "F109m" "F109s" "F110m" "F110s" "F111s"
## [89] "F112m" "F112s" "F113m" "F113s" "F114m" "F115m" "F115s" "F117m"
## [97] "F119s" "F120m" "F120s" "F121m" "F121s" "F122m" "F122s" "F125m"
## [105] "F128s" "F129s" "F130s" "F131s" "F132m" "F132s" "F133m" "F133s"
## [113] "F134s" "F139s" "F140s" "F141m" "F141s" "F142m" "F142s" "F145s"
## [121] "F149s" "F150m" "F150s" "F151m" "F151s" "F152s" "F153s" "F155m"
## [129] "F158s" "F159s" "F161s" "F162m" "F162s" "F163m" "F165m" "F168s"
## [137] "F170m" "F170s" "F171m" "F171s" "F172m" "F172s" "F173m" "F173s"
## [145] "F174s" "F179s" "F181s" "F182s" "F185m" "F189s" "F190s" "F191m"
## [153] "F191s" "F192m" "F192s" "F193m" "F193s" "F194s" "F195m" "F195s"
## [161] "F198m" "F198s" "F199m" "F199s" "F20m" "F20s" "F200m" "F200s"
## [169] "F201m" "F202m" "F202s" "F203m" "F204m" "F204s" "F205m" "F205s"
## [177] "F206m" "F206s" "F208m" "F208s" "F209m" "F209s" "F21m" "F21s"
## [185] "F220m" "F220s" "F228m" "F228s" "F229m" "F229s" "F23s" "F230m"
## [193] "F230s" "F231m" "F231s" "F232m" "F233m" "F233s" "F238m" "F239m"
## [201] "F239s" "F24m" "F250m" "F250s" "F251m" "F251s" "F252m" "F252s"
## [209] "F258m" "F258s" "F259m" "F259s" "F28m" "F28s" "F29m" "F29s"
## [217] "F300m" "F300s" "F301m" "F301s" "F302m" "F302s" "F308m" "F308s"
## [225] "F309m" "F309s" "F310m" "F310s" "F311m" "F311s" "F312m" "F312s"
## [233] "F313m" "F313s" "F314m" "F314s" "F315m" "F315s" "F316m" "F316s"
## [241] "F317m" "F317s" "F318m" "F318s" "F319m" "F319s" "F32m" "F320m"
## [249] "F320s" "F321m" "F321s" "F322m" "F322s" "F323m" "F323s" "F328m"
## [257] "F328s" "F329m" "F329s" "F330m" "F330s" "F331m" "F331s" "F332m"
## [265] "F332s" "F333m" "F333s" "F334m" "F334s" "F338m" "F338s" "F339m"
## [273] "F339s" "F340m" "F340s" "F341m" "F341s" "F348m" "F348s" "F349s"
## [281] "F380m" "F380s" "F381s" "F388m" "F388s" "F39m" "F39s" "F400m"
## [289] "F400s" "F401m" "F401s" "F402m" "F402s" "F408m" "F408s" "F409s"
## [297] "F410m" "F410s" "F411m" "F411s" "F412m" "F412s" "F413m" "F413s"
## [305] "F418m" "F418s" "F419m" "F419s" "F420m" "F420s" "F421m" "F421s"
## [313] "F422m" "F422s" "F428m" "F428s" "F429m" "F429s" "F430m" "F430s"
## [321] "F431m" "F431s" "F432m" "F432s" "F438m" "F438s" "F439m" "F439s"
## [329] "F440m" "F440s" "F441m" "F441s" "F443m" "F443s" "F444m" "F444s"
## [337] "F445m" "F445s" "F446m" "F446s" "F447m" "F448m" "F448s" "F449m"
## [345] "F449s" "F450m" "F450s" "F451s" "F452m" "F452s" "F453m" "F453s"
## [353] "F454m" "F454s" "F458m" "F458s" "F459m" "F459s" "F480m" "F480s"
## [361] "F481s" "F488m" "F488s" "F489m" "F489s" "F500m" "F500s" "F501m"
## [369] "F501s" "F502m" "F502s" "F505m" "F505s" "F508m" "F508s" "F509m"
## [377] "F509s" "F510m" "F510s" "F511m" "F511s" "F512s" "F513m" "F513s"
## [385] "F514m" "F514s" "F515m" "F515s" "F519m" "F519s" "F520m" "F520s"
## [393] "F521s" "F522m" "F522s" "F524m" "F524s" "F526m" "F526s" "F527m"
## [401] "F527s" "F528m" "F529m" "F529s" "F530m" "F530s" "F531m" "F531s"
## [409] "F538s" "F539m" "F54m" "F54s" "F55s" "F59m" "F59s" "F600m"
## [417] "F600s" "F601m" "F601s" "F602m" "F602s" "F603m" "F603s" "F604m"
## [425] "F604s" "F605m" "F605s" "F606m" "F606s" "F607m" "F607s" "F608m"
## [433] "F608s" "F609m" "F609s" "F61m" "F61s" "F620m" "F620s" "F621m"
## [441] "F621s" "F628m" "F628s" "F629m" "F629s" "F630m" "F630s" "F631s"
## [449] "F633m" "F633s" "F638s" "F639s" "F640m" "F640s" "F641s" "F648m"
## [457] "F649s" "F650s" "F659s" "F660s" "F661s" "F669s" "F680s" "F681m"
## [465] "F681s" "F69m" "F69s" "F700m" "F700s" "F701m" "F708m" "F709m"
## [473] "F709s" "F711s" "F719s" "F729s" "F789m" "F789s" "F790s" "F799s"
## [481] "F800m" "F800s" "F801m" "F801s" "F802m" "F802s" "F803s" "F809s"
## [489] "F810m" "F810s" "F812s" "F819m" "F819s" "F82m" "F82s" "F840s"
## [497] "F841m" "F841s" "F843s" "F845m" "F845s" "F89s" "F900s" "F911s"
## [505] "F918m" "F918s" "F919m" "F919s" "F920s" "F929s" "F940s" "F950s"
## [513] "F951m" "F951s" "F952s" "F959s" "F981m" "F985m" "F985s" "F988s"
## [521] "F99m" "F99s"Create summary column
psychiatric_no_duplicate$ICD.psychiatric.raw <-
apply(
psychiatric_no_duplicate[,2:ncol(psychiatric_no_duplicate)] == 1,
1,
any)
psychiatric_no_duplicate$ICD.psychiatric <-
as.integer(
psychiatric_no_duplicate$ICD.psychiatric.raw
)
psychiatric_reduced <- psychiatric_no_duplicate %>%
select(IID, ICD.psychiatric)Summary
summary(as.factor(psychiatric_reduced$ICD.psychiatric))## 0 1
## 463308 39311Merge all data frames
ICD10.dx.groups <- cbind(
autoimmune_reduced,
autoinflammatory_reduced,
immunodeficiency_reduced,
memory_reduced,
metabolic_reduced,
psychiatric_reduced
)Summary
summary(ICD10.dx.groups)## IID ICD.autoimmune IID ICD.autoinflammatory
## Min. :1000015 Min. :0.0000 Min. :1000015 Min. :0.0000
## 1st Qu.:2256558 1st Qu.:0.0000 1st Qu.:2256558 1st Qu.:0.0000
## Median :3513105 Median :0.0000 Median :3513105 Median :0.0000
## Mean :3513104 Mean :0.0836 Mean :3513104 Mean :0.2986
## 3rd Qu.:4769650 3rd Qu.:0.0000 3rd Qu.:4769650 3rd Qu.:1.0000
## Max. :6026196 Max. :1.0000 Max. :6026196 Max. :1.0000
## IID ICD.immunodeficiency IID
## Min. :1000015 Min. :0.000000 Min. :1000015
## 1st Qu.:2256558 1st Qu.:0.000000 1st Qu.:2256558
## Median :3513105 Median :0.000000 Median :3513105
## Mean :3513104 Mean :0.001132 Mean :3513104
## 3rd Qu.:4769650 3rd Qu.:0.000000 3rd Qu.:4769650
## Max. :6026196 Max. :1.000000 Max. :6026196
## ICD.memory IID ICD.metabolic IID
## Min. :0.000000 Min. :1000015 Min. :0.0000 Min. :1000015
## 1st Qu.:0.000000 1st Qu.:2256558 1st Qu.:0.0000 1st Qu.:2256558
## Median :0.000000 Median :3513105 Median :0.0000 Median :3513105
## Mean :0.009462 Mean :3513104 Mean :0.1679 Mean :3513104
## 3rd Qu.:0.000000 3rd Qu.:4769650 3rd Qu.:0.0000 3rd Qu.:4769650
## Max. :1.000000 Max. :6026196 Max. :1.0000 Max. :6026196
## ICD.psychiatric
## Min. :0.00000
## 1st Qu.:0.00000
## Median :0.00000
## Mean :0.07821
## 3rd Qu.:0.00000
## Max. :1.00000ICD10.dx.groups_no_duplicate <- ICD10.dx.groups[!duplicated(as.list(ICD10.dx.groups))]
ICD10.dx.groups_no_duplicate$ICD.immunodysregulation.raw <-
with(ICD10.dx.groups_no_duplicate,
if_else(condition = ICD.autoimmune == 1 | ICD.autoinflammatory == 1 | ICD.immunodeficiency == 1,
1,
0)
)
ICD10.dx.groups_no_duplicate$ICD.immunodysregulation <-
as.integer(
ICD10.dx.groups_no_duplicate$ICD.immunodysregulation.raw
)
ICD10.dx.groups_no_duplicate$ICD.immunodysregulation.raw <- NULL
summarytools::freq(ICD10.dx.groups_no_duplicate[,-1])## Frequencies
## ICD10.dx.groups_no_duplicate$ICD.autoimmune
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- -------- --------- -------------- --------- --------------
## 0 460600 91.64 91.64 91.64 91.64
## 1 42019 8.36 100.00 8.36 100.00
## <NA> 0 0.00 100.00
## Total 502619 100.00 100.00 100.00 100.00
##
## ICD10.dx.groups_no_duplicate$ICD.autoinflammatory
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- -------- --------- -------------- --------- --------------
## 0 352522 70.14 70.14 70.14 70.14
## 1 150097 29.86 100.00 29.86 100.00
## <NA> 0 0.00 100.00
## Total 502619 100.00 100.00 100.00 100.00
##
## ICD10.dx.groups_no_duplicate$ICD.immunodeficiency
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- -------- --------- -------------- --------- --------------
## 0 502050 99.89 99.89 99.89 99.89
## 1 569 0.11 100.00 0.11 100.00
## <NA> 0 0.00 100.00
## Total 502619 100.00 100.00 100.00 100.00
##
## ICD10.dx.groups_no_duplicate$ICD.memory
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- -------- --------- -------------- --------- --------------
## 0 497863 99.05 99.05 99.05 99.05
## 1 4756 0.95 100.00 0.95 100.00
## <NA> 0 0.00 100.00
## Total 502619 100.00 100.00 100.00 100.00
##
## ICD10.dx.groups_no_duplicate$ICD.metabolic
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- -------- --------- -------------- --------- --------------
## 0 418254 83.21 83.21 83.21 83.21
## 1 84365 16.79 100.00 16.79 100.00
## <NA> 0 0.00 100.00
## Total 502619 100.00 100.00 100.00 100.00
##
## ICD10.dx.groups_no_duplicate$ICD.psychiatric
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- -------- --------- -------------- --------- --------------
## 0 463308 92.18 92.18 92.18 92.18
## 1 39311 7.82 100.00 7.82 100.00
## <NA> 0 0.00 100.00
## Total 502619 100.00 100.00 100.00 100.00
##
## ICD10.dx.groups_no_duplicate$ICD.immunodysregulation
##
## Freq % Valid % Valid Cum. % Total % Total Cum.
## ----------- -------- --------- -------------- --------- --------------
## 0 345450 68.73 68.73 68.73 68.73
## 1 157169 31.27 100.00 31.27 100.00
## <NA> 0 0.00 100.00
## Total 502619 100.00 100.00 100.00 100.00UpSetR plot
UpSetR::upset(
data = ICD10.dx.groups_no_duplicate,
nintersects = NA,
sets = colnames(ICD10.dx.groups_no_duplicate[,2:ncol(ICD10.dx.groups_no_duplicate)]))
pdf(file = "inflammatory_autoimmune/dx.upset.pdf", width = 13, height = 7)
UpSetR::upset(
data = ICD10.dx.groups_no_duplicate,
nintersects = NA,
sets = colnames(ICD10.dx.groups_no_duplicate[,2:ncol(ICD10.dx.groups_no_duplicate)]))
dev.off()## quartz_off_screen
## 2Export data frame
write.table(x = ICD10.dx.groups_no_duplicate, file = "inflammatory_autoimmune/ICD.dx.txt",
quote = F, row.names = F, col.names = T)