Checking subtype information

library(TCGAbiolinks)
library(plyr)
library(dplyr)
library(SummarizedExperiment)

1 Retrieve the data

query <- GDCquery(project = "TCGA-COAD",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification", 
                  workflow.type = "HTSeq - FPKM-UQ")
GDCdownload(query)
data <- GDCprepare(query)
metadata <- colData(data) %>% as.data.frame() %>% dplyr::filter(definition == "Primary solid Tumor")
subtype <- TCGAbiolinks::TCGAquery_subtype("COAD")

## [1] 276  45

## [1] 478 111

2 MSI differencies

## 
##                       MSI-H         MSI-L           MSS Not Evaluable 
##             0            38            44           193             1

## 
##                       MSI-H         MSI-L           MSS Not Evaluable 
##             0            40            42           126             0

3 Samples difference

# Samples in he data but not in the subtype
setdiff(metadata$patient,subtype$patient)

##   [1] "TCGA-AZ-6601" "TCGA-AZ-6606" "TCGA-A6-6137" "TCGA-CM-5860" "TCGA-F4-6569"
##   [6] "TCGA-F4-6461" "TCGA-D5-6927" "TCGA-CK-5913" "TCGA-AZ-6605" "TCGA-A6-6780"
##  [11] "TCGA-NH-A6GB" "TCGA-AY-6386" "TCGA-D5-6539" "TCGA-CA-5796" "TCGA-A6-5660"
##  [16] "TCGA-D5-6926" "TCGA-CM-6679" "TCGA-G4-6628" "TCGA-F4-6808" "TCGA-G4-6309"
##  [21] "TCGA-G4-6586" "TCGA-AZ-6600" "TCGA-NH-A8F7" "TCGA-D5-6932" "TCGA-D5-6931"
##  [26] "TCGA-A6-5656" "TCGA-AM-5820" "TCGA-A6-6142" "TCGA-G4-6311" "TCGA-D5-6535"
##  [31] "TCGA-G4-6303" "TCGA-F4-6703" "TCGA-A6-2675" "TCGA-A6-5661" "TCGA-DM-A28A"
##  [36] "TCGA-AZ-6599" "TCGA-DM-A1HB" "TCGA-G4-6310" "TCGA-D5-6531" "TCGA-CM-6164"
##  [41] "TCGA-F4-6854" "TCGA-AA-3713" "TCGA-DM-A285" "TCGA-G4-6315" "TCGA-A6-6781"
##  [46] "TCGA-A6-6653" "TCGA-5M-AAT6" "TCGA-D5-6928" "TCGA-AA-3712" "TCGA-AZ-6607"
##  [51] "TCGA-A6-5657" "TCGA-G4-6302" "TCGA-NH-A6GC" "TCGA-QG-A5YV" "TCGA-CK-5912"
##  [56] "TCGA-AA-3496" "TCGA-NH-A6GA" "TCGA-CK-6751" "TCGA-5M-AAT4" "TCGA-CM-6675"
##  [61] "TCGA-CK-6747" "TCGA-AY-6197" "TCGA-AD-A5EJ" "TCGA-G4-6314" "TCGA-CK-5916"
##  [66] "TCGA-4T-AA8H" "TCGA-CM-6678" "TCGA-NH-A8F8" "TCGA-F4-6855" "TCGA-RU-A8FL"
##  [71] "TCGA-A6-5659" "TCGA-D5-6532" "TCGA-A6-6140" "TCGA-NH-A50U" "TCGA-A6-4105"
##  [76] "TCGA-A6-A5ZU" "TCGA-QG-A5YW" "TCGA-D5-6920" "TCGA-AD-6890" "TCGA-AD-6963"
##  [81] "TCGA-D5-5537" "TCGA-AZ-6603" "TCGA-NH-A50T" "TCGA-D5-6529" "TCGA-G4-6317"
##  [86] "TCGA-CM-6165" "TCGA-F4-6807" "TCGA-DM-A1D4" "TCGA-G4-6307" "TCGA-G4-6299"
##  [91] "TCGA-D5-7000" "TCGA-DM-A28F" "TCGA-DM-A1D8" "TCGA-A6-6651" "TCGA-D5-5540"
##  [96] "TCGA-F4-6809" "TCGA-DM-A280" "TCGA-NH-A5IV" "TCGA-A6-5662" "TCGA-A6-6648"
## [101] "TCGA-CM-6168" "TCGA-AZ-4323" "TCGA-G4-6626" "TCGA-DM-A1DA" "TCGA-A6-A566"
## [106] "TCGA-CM-5863" "TCGA-AA-3660" "TCGA-CA-6716" "TCGA-CK-6746" "TCGA-CA-6715"
## [111] "TCGA-DM-A288" "TCGA-D5-6530" "TCGA-D5-6534" "TCGA-D5-5539" "TCGA-AU-3779"
## [116] "TCGA-A6-6649" "TCGA-AA-3663" "TCGA-CM-5861" "TCGA-F4-6463" "TCGA-CM-4743"
## [121] "TCGA-D5-6541" "TCGA-AD-6964" "TCGA-5M-AAT5" "TCGA-T9-A92H" "TCGA-A6-A56B"
## [126] "TCGA-AD-5900" "TCGA-QL-A97D" "TCGA-G4-6588" "TCGA-CA-5797" "TCGA-DM-A282"
## [131] "TCGA-CM-6166" "TCGA-AZ-4616" "TCGA-CM-5348" "TCGA-G4-6298" "TCGA-AA-3489"
## [136] "TCGA-AU-6004" "TCGA-4N-A93T" "TCGA-CA-6719" "TCGA-AA-3655" "TCGA-G4-6627"
## [141] "TCGA-D5-6540" "TCGA-CK-4947" "TCGA-A6-5665" "TCGA-CA-6718" "TCGA-AD-6548"
## [146] "TCGA-F4-6704" "TCGA-A6-6652" "TCGA-AD-6899" "TCGA-CM-6170" "TCGA-D5-6537"
## [151] "TCGA-F4-6570" "TCGA-5M-AATE" "TCGA-F4-6806" "TCGA-G4-6295" "TCGA-DM-A28M"
## [156] "TCGA-WS-AB45" "TCGA-AA-3697" "TCGA-A6-6650" "TCGA-AZ-5403" "TCGA-CK-4948"
## [161] "TCGA-CK-4950" "TCGA-CM-5864" "TCGA-AA-3662" "TCGA-D5-6536" "TCGA-AY-5543"
## [166] "TCGA-AD-6888" "TCGA-F4-6805" "TCGA-DM-A1D6" "TCGA-DM-A1D9" "TCGA-G4-6321"
## [171] "TCGA-CM-6161" "TCGA-G4-6297" "TCGA-A6-6138" "TCGA-CM-6169" "TCGA-DM-A1HA"
## [176] "TCGA-DM-A1D0" "TCGA-A6-A565" "TCGA-G4-6306" "TCGA-A6-A567" "TCGA-CA-6717"
## [181] "TCGA-D5-6538" "TCGA-DM-A28H" "TCGA-A6-6782" "TCGA-G4-6320" "TCGA-CM-5349"
## [186] "TCGA-CM-4751" "TCGA-G4-6323" "TCGA-SS-A7HO" "TCGA-D5-5541" "TCGA-A6-6654"
## [191] "TCGA-CM-5868" "TCGA-AD-6901" "TCGA-AA-3511" "TCGA-CM-6172" "TCGA-DM-A28G"
## [196] "TCGA-CM-6171" "TCGA-CM-6676" "TCGA-CM-5862" "TCGA-AD-A5EK" "TCGA-AY-A71X"
## [201] "TCGA-AZ-6608" "TCGA-QG-A5Z1" "TCGA-CA-5254" "TCGA-AD-6895" "TCGA-D5-6922"
## [206] "TCGA-F4-6459" "TCGA-G4-6294" "TCGA-QG-A5Z2" "TCGA-DM-A0XF" "TCGA-CM-6677"
## [211] "TCGA-DM-A28E" "TCGA-D5-6923" "TCGA-CK-6748" "TCGA-NH-A50V" "TCGA-A6-6141"
## [216] "TCGA-G4-6304" "TCGA-D5-6929" "TCGA-CM-6674" "TCGA-D5-6930" "TCGA-CM-6162"
## [221] "TCGA-F4-6856" "TCGA-QG-A5YX" "TCGA-AM-5821" "TCGA-AZ-5407" "TCGA-D5-6533"
## [226] "TCGA-DM-A0XD" "TCGA-A6-5667" "TCGA-CM-5344" "TCGA-CM-6167" "TCGA-A6-5666"
## [231] "TCGA-CK-5914" "TCGA-DM-A0X9" "TCGA-F4-6460" "TCGA-DM-A1DB" "TCGA-D5-5538"
## [236] "TCGA-AD-6889" "TCGA-DM-A1D7" "TCGA-AY-A54L" "TCGA-3L-AA1B" "TCGA-CM-6163"
## [241] "TCGA-AY-A69D" "TCGA-AY-A8YK" "TCGA-CA-5255" "TCGA-CK-4952" "TCGA-CK-5915"
## [246] "TCGA-DM-A28K" "TCGA-G4-6322" "TCGA-G4-6293" "TCGA-D5-6924" "TCGA-DM-A28C"
## [251] "TCGA-AY-6196" "TCGA-D5-6898" "TCGA-A6-5664" "TCGA-CM-6680" "TCGA-AZ-6598"
## [256] "TCGA-5M-AATA" "TCGA-AD-6965" "TCGA-G4-6625"

# Samples in subtype but not in the data
setdiff(subtype$patient,metadata$patient) 

##  [1] "TCGA-A6-2670" "TCGA-AA-3558" "TCGA-AA-3695" "TCGA-AF-2689" "TCGA-AF-2691"
##  [6] "TCGA-AF-2692" "TCGA-AF-3400" "TCGA-AF-3913" "TCGA-AG-3574" "TCGA-AG-3575"
## [11] "TCGA-AG-3578" "TCGA-AG-3580" "TCGA-AG-3581" "TCGA-AG-3582" "TCGA-AG-3583"
## [16] "TCGA-AG-3584" "TCGA-AG-3586" "TCGA-AG-3587" "TCGA-AG-3593" "TCGA-AG-3594"
## [21] "TCGA-AG-3598" "TCGA-AG-3599" "TCGA-AG-3600" "TCGA-AG-3601" "TCGA-AG-3602"
## [26] "TCGA-AG-3605" "TCGA-AG-3608" "TCGA-AG-3609" "TCGA-AG-3611" "TCGA-AG-3612"
## [31] "TCGA-AG-3726" "TCGA-AG-3727" "TCGA-AG-3728" "TCGA-AG-3878" "TCGA-AG-3881"
## [36] "TCGA-AG-3882" "TCGA-AG-3883" "TCGA-AG-3885" "TCGA-AG-3887" "TCGA-AG-3890"
## [41] "TCGA-AG-3892" "TCGA-AG-3893" "TCGA-AG-3894" "TCGA-AG-3896" "TCGA-AG-3898"
## [46] "TCGA-AG-3901" "TCGA-AG-3902" "TCGA-AG-3909" "TCGA-AG-3999" "TCGA-AG-4001"
## [51] "TCGA-AG-4005" "TCGA-AG-4007" "TCGA-AG-4008" "TCGA-AG-4015" "TCGA-AG-A002"
## [56] "TCGA-AG-A008" "TCGA-AG-A00C" "TCGA-AG-A00H" "TCGA-AG-A00Y" "TCGA-AG-A011"
## [61] "TCGA-AG-A014" "TCGA-AG-A015" "TCGA-AG-A016" "TCGA-AG-A01J" "TCGA-AG-A01L"
## [66] "TCGA-AG-A01N" "TCGA-AG-A01W" "TCGA-AG-A01Y" "TCGA-AG-A020" "TCGA-AG-A023"
## [71] "TCGA-AG-A025" "TCGA-AG-A026" "TCGA-AG-A02G" "TCGA-AG-A02N" "TCGA-AG-A02X"
## [76] "TCGA-AG-A032" "TCGA-AG-A036" "TCGA-AZ-4681"

4 Check for replicates

metadata$patient %>% duplicated %>% table

## .
## FALSE  TRUE 
##   456    22

sort(metadata$sample[metadata$patient %in% metadata$patient[metadata$patient %>% duplicated]])

##  [1] "TCGA-A6-2672-01A" "TCGA-A6-2672-01B" "TCGA-A6-2674-01A" "TCGA-A6-2674-01A"
##  [5] "TCGA-A6-2674-01B" "TCGA-A6-2677-01A" "TCGA-A6-2677-01B" "TCGA-A6-2684-01A"
##  [9] "TCGA-A6-2684-01A" "TCGA-A6-2684-01C" "TCGA-A6-3809-01A" "TCGA-A6-3809-01A"
## [13] "TCGA-A6-3809-01B" "TCGA-A6-3810-01A" "TCGA-A6-3810-01A" "TCGA-A6-3810-01B"
## [17] "TCGA-A6-5656-01A" "TCGA-A6-5656-01A" "TCGA-A6-5656-01B" "TCGA-A6-5659-01A"
## [21] "TCGA-A6-5659-01A" "TCGA-A6-5659-01B" "TCGA-A6-5661-01A" "TCGA-A6-5661-01B"
## [25] "TCGA-A6-5665-01A" "TCGA-A6-5665-01B" "TCGA-A6-6650-01A" "TCGA-A6-6650-01A"
## [29] "TCGA-A6-6650-01B" "TCGA-A6-6780-01A" "TCGA-A6-6780-01A" "TCGA-A6-6780-01B"
## [33] "TCGA-A6-6781-01A" "TCGA-A6-6781-01A" "TCGA-A6-6781-01B"

5 Check survival

common.samples <- intersect(metadata$patient,subtype$patient)
metadata[metadata$patient == common.samples[1],grep("vital|follow|death",colnames(metadata))]

subtype[subtype$patient == common.samples[1],grep("vital|follow|death",colnames(subtype))]

6 Session Information

## R Under development (unstable) (2020-02-25 r77857)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.3
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] SummarizedExperiment_1.17.3 DelayedArray_0.13.4        
##  [3] BiocParallel_1.21.2         matrixStats_0.55.0         
##  [5] Biobase_2.47.2              GenomicRanges_1.39.2       
##  [7] GenomeInfoDb_1.23.13        IRanges_2.21.3             
##  [9] S4Vectors_0.25.12           BiocGenerics_0.33.0        
## [11] dplyr_0.8.4                 plyr_1.8.5                 
## [13] TCGAbiolinks_2.15.3        
## 
## loaded via a namespace (and not attached):
##   [1] pkgcond_0.1.0            colorspace_1.4-1         ggsignif_0.6.0          
##   [4] selectr_0.4-2            hwriter_1.3.2            testextra_0.1.0.1       
##   [7] XVector_0.27.0           base64enc_0.1-3          ggpubr_0.2.5            
##  [10] ggrepel_0.8.1            bit64_0.9-7              AnnotationDbi_1.49.1    
##  [13] xml2_1.2.2               codetools_0.2-16         splines_4.0.0           
##  [16] R.methodsS3_1.8.0        doParallel_1.0.15        DESeq_1.39.0            
##  [19] geneplotter_1.65.0       knitr_1.28               jsonlite_1.6.1          
##  [22] Rsamtools_2.3.5          km.ci_0.5-2              broom_0.5.4             
##  [25] annotate_1.65.1          dbplyr_1.4.2             png_0.1-7               
##  [28] R.oo_1.23.0              readr_1.3.1              compiler_4.0.0          
##  [31] httr_1.4.1               backports_1.1.5          assertthat_0.2.1        
##  [34] Matrix_1.2-18            lazyeval_0.2.2           limma_3.43.4            
##  [37] htmltools_0.4.0          prettyunits_1.1.1        tools_4.0.0             
##  [40] gtable_0.3.0             glue_1.3.1               GenomeInfoDbData_1.2.2  
##  [43] ggthemes_4.2.0           rappdirs_0.3.1           ShortRead_1.45.3        
##  [46] Rcpp_1.0.3               vctrs_0.2.3              Biostrings_2.55.4       
##  [49] nlme_3.1-144             rtracklayer_1.47.0       iterators_1.0.12        
##  [52] xfun_0.12                stringr_1.4.0            testthat_2.3.1          
##  [55] rvest_0.3.5              lifecycle_0.1.0          XML_3.99-0.3            
##  [58] edgeR_3.29.0             zoo_1.8-7                postlogic_0.1.0.1       
##  [61] zlibbioc_1.33.1          scales_1.1.0             aroma.light_3.17.1      
##  [64] hms_0.5.3                RColorBrewer_1.1-2       yaml_2.2.1              
##  [67] curl_4.3                 memoise_1.1.0            gridExtra_2.3           
##  [70] KMsurv_0.1-5             ggplot2_3.2.1            downloader_0.4          
##  [73] biomaRt_2.43.3           latticeExtra_0.6-29      stringi_1.4.6           
##  [76] RSQLite_2.2.0            genefilter_1.69.0        foreach_1.4.8           
##  [79] GenomicFeatures_1.39.5   rlang_0.4.4              pkgconfig_2.0.3         
##  [82] bitops_1.0-6             evaluate_0.14            lattice_0.20-40         
##  [85] purrr_0.3.3              GenomicAlignments_1.23.1 bit_1.1-15.2            
##  [88] tidyselect_1.0.0         magrittr_1.5             R6_2.4.1                
##  [91] generics_0.0.2           DBI_1.1.0                mgcv_1.8-31             
##  [94] pillar_1.4.3             survival_3.1-8           RCurl_1.98-1.1          
##  [97] tibble_2.1.3             EDASeq_2.21.0            crayon_1.3.4            
## [100] survMisc_0.5.5           purrrogress_0.1.1        BiocFileCache_1.11.4    
## [103] rmarkdown_2.1            jpeg_0.1-8.1             progress_1.2.2          
## [106] locfit_1.5-9.1           grid_4.0.0               sva_3.35.0              
## [109] data.table_1.12.9        blob_1.2.1               digest_0.6.25           
## [112] xtable_1.8-4             tidyr_1.0.2              R.utils_2.9.2           
## [115] openssl_1.4.1            munsell_0.5.0            survminer_0.4.6         
## [118] parsetools_0.1.1         askpass_1.1