R Notebook
GWAS replication study in R
- So as a graduate student at umkc, we got introduced to the concept of GWAS (genome wide association studies). in my first go using my linux system, i failed at it since i did not know what the output files meant and also i really had no idea what to do with the data.
- I still dont fully understand GWAS but I was able to replicate this study and will begin diving deeper into the data to better understand gwas.
- Here is a recap of the replication study and I will expound some more with a new document after understanding more things if not most things about GWAS and how i can contribute to this technique.
Preparing data for GWAS
- Two files are needed to start a GWAS
- A .map file and ,ped
- i think that is all needed to start a gwas
- the plink .exe file needs to be present in the folder of the needed files
- the trick for me was to use the cmd to load the gwas file to make the bed file
- open a powershell terminal from the folder of the adgwas (Right click in the folder and then open a powershell or cmd and that is the only way it works)
- This is the line used './plink --file adgwas --make-bed --out output/binary_adgwas'
- remember to have the output folder in the gwas folder to prevent clutter
- you should then have a bunch of binary files in the output folder
- The use of these files i am yet to figure outPreparing for GWAS by working on folders and neatness of the setup
library(plinkQC)
package.dir <- find.package('plinkQC')
# Dir where data is stored
#setwd('dir of gwas data = your personal directory')
indir <- paste(getwd(), '/input', sep='')
qcdir <- paste(getwd(), '/output', sep='')
# The steps below i suppose are for if you did not use the powershell to make the binary files
## Follow the steps below if you dont know how to use the powersheel
# Prefix of the binary PLINK files (*.bim, *.bed, *.fam)
name <- 'binary_adgwas'
# Change this dir to PLINK location on your PC!
path2plink <- "C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/plink/plink.exe"
# Make PLINK binary files (raw.bim, raw.bam, raw.fam) from the text ones (adgwas.ped, adgwas.map)
#make_binary = paste(path2plink, ' --file ', indir, '/adgwas --make-bed --out ', indir, '/raw', sep="")
#system(make_binary, intern=TRUE)Individual QC
#Check sex-ensure that observed or assigned (counted males vs females) and reported
# sex or genders are consistent. Assigned sex male or female vs SNP sex (Xchr location)
fail_sex <- check_sex(indir, name, qcdir = qcdir, path2plink = path2plink,
showPlinkOutput = TRUE, verbose=TRUE)## Run check_sex via plink --check-sex## PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
## (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.log.
## Options in effect:
## --bfile C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas
## --check-sex
## --out C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas
##
## 15775 MB RAM detected; reserving 7887 MB for main workspace.
## 380157 variants loaded from .bim file.
## 364 people (191 males, 173 females) loaded from .fam.
## 364 phenotype values loaded from .fam.
## Using 1 thread (no multithreaded calculations invoked).
## Before main variant filters, 364 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.975068.
## 380157 variants and 364 people pass filters and QC.
## Among remaining phenotypes, 176 are cases and 188 are controls.
## --check-sex: 7904 Xchr and 0 Ychr variant(s) scanned, no problems detected.
## Report written to
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.sexcheck
## .run_check_sex(indir, name, qcdir = qcdir, path2plink = path2plink,
showPlinkOutput = TRUE, verbose=TRUE)## Run check_sex via plink --check-sex## PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
## (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.log.
## Options in effect:
## --bfile C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas
## --check-sex
## --out C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas
##
## 15775 MB RAM detected; reserving 7887 MB for main workspace.
## 380157 variants loaded from .bim file.
## 364 people (191 males, 173 females) loaded from .fam.
## 364 phenotype values loaded from .fam.
## Using 1 thread (no multithreaded calculations invoked).
## Before main variant filters, 364 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.975068.
## 380157 variants and 364 people pass filters and QC.
## Among remaining phenotypes, 176 are cases and 188 are controls.
## --check-sex: 7904 Xchr and 0 Ychr variant(s) scanned, no problems detected.
## Report written to
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.sexcheck
## .## [1] 0#outlying missing genotypes and heterozygosity rate
fail_het_imiss <- check_het_and_miss(indir, qcdir = qcdir, name=name, path2plink = path2plink,
imissTh = 0.1, hetTh = 3,
interactive = FALSE, verbose = TRUE, showPlinkOutput = TRUE)## Run check_heterozygosity via plink --het## PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
## (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.log.
## Options in effect:
## --bfile C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas
## --het
## --out C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas
##
## 15775 MB RAM detected; reserving 7887 MB for main workspace.
## 380157 variants loaded from .bim file.
## 364 people (191 males, 173 females) loaded from .fam.
## 364 phenotype values loaded from .fam.
## Using 1 thread (no multithreaded calculations invoked).
## Before main variant filters, 364 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.975068.
## 380157 variants and 364 people pass filters and QC.
## Among remaining phenotypes, 176 are cases and 188 are controls.
## --het: 372253 variants scanned, report written to
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.het
## .## Run check_missingness via plink --missing## PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
## (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.log.
## Options in effect:
## --bfile C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas
## --missing
## --out C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas
##
## 15775 MB RAM detected; reserving 7887 MB for main workspace.
## 380157 variants loaded from .bim file.
## 364 people (191 males, 173 females) loaded from .fam.
## 364 phenotype values loaded from .fam.
## Using 1 thread (no multithreaded calculations invoked).
## Before main variant filters, 364 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.975068.
## --missing: Sample missing data report written to
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.imiss,
## and variant-based missing data report written to
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.lmiss.#remove ibd data points- genotypes are not a good representation of the population
exclude_relatedness <- check_relatedness(indir, name, qcdir = qcdir, path2plink=path2plink,
highIBDTh=0.2,
interactive=TRUE, verbose=FALSE, showPlinkOutput = TRUE)## PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
## (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.log.
## Options in effect:
## --bfile C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas
## --exclude range C:/Users/GrandProf/AppData/Local/R/win-library/4.2/plinkQC/extdata/high-LD-regions-hg19-GRCh37.txt
## --indep-pairwise 50 5 0.2
## --out C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas
##
## 15775 MB RAM detected; reserving 7887 MB for main workspace.
## 380157 variants loaded from .bim file.
## 364 people (191 males, 173 females) loaded from .fam.
## 364 phenotype values loaded from .fam.
## --exclude range: 8098 variants excluded.
## --exclude range: 372059 variants remaining.
## Using 1 thread (no multithreaded calculations invoked).
## Before main variant filters, 364 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.9751.
## 372059 variants and 364 people pass filters and QC.
## Among remaining phenotypes, 176 are cases and 188 are controls.
##
1%
2%
3%
3%
4%
5%
6%
7%
8%
8%
9%
10%
11%
12%
13%
13%
14%
15%
16%
17%
18%
19%
20%
21%
22%
23%
23%
24%
25%
26%
27%
28%
28%
29%
30%
31%
32%
33%
33%
34%
35%
36%
37%
38%
38%
39%
40%
41%
42%
43%
43%
44%
45%
46%
47%
48%
48%
49%
50%
51%
52%
53%
53%
54%
55%
56%
57%
58%
58%
59%
60%
61%
62%
63%
63%
64%
65%
66%
67%
68%
68%
69%
70%
71%
72%
73%
73%
74%
75%
76%
77%
78%
78%
79%
80%
81%
82%
83%
83%
84%
85%
86%
87%
88%
88%
89%
90%
91%
92%
93%
93%
94%
95%
96%
97%
98%
98%
99%
Pruned 22065 variants from chromosome 1, leaving 7539.
##
1%
2%
3%
4%
5%
6%
7%
8%
9%
10%
11%
12%
13%
14%
15%
15%
16%
17%
18%
18%
19%
20%
21%
21%
22%
23%
24%
24%
25%
26%
27%
27%
28%
29%
30%
30%
31%
32%
33%
33%
34%
35%
36%
37%
38%
39%
40%
41%
44%
45%
45%
46%
47%
48%
48%
49%
50%
51%
51%
52%
53%
54%
54%
55%
56%
57%
58%
59%
60%
61%
62%
63%
64%
65%
66%
67%
68%
69%
70%
71%
72%
73%
73%
74%
75%
76%
78%
79%
80%
80%
81%
82%
83%
83%
84%
85%
86%
87%
88%
89%
90%
91%
92%
93%
94%
95%
96%
97%
98%
99%
Pruned 22603 variants from chromosome 2, leaving 7188.
##
0%
1%
1%
2%
3%
4%
5%
6%
7%
8%
9%
10%
11%
11%
12%
12%
13%
14%
15%
16%
17%
18%
19%
20%
21%
22%
22%
23%
23%
24%
25%
26%
27%
28%
29%
29%
30%
30%
31%
32%
33%
34%
35%
36%
37%
38%
39%
40%
40%
41%
41%
42%
43%
44%
45%
46%
47%
49%
50%
51%
52%
53%
53%
54%
54%
55%
56%
57%
58%
59%
60%
61%
62%
63%
64%
64%
65%
65%
66%
67%
68%
69%
70%
71%
72%
73%
74%
75%
75%
76%
76%
77%
78%
79%
80%
81%
82%
83%
84%
85%
86%
86%
87%
87%
88%
89%
90%
91%
92%
93%
94%
95%
96%
97%
97%
98%
98%
99%
Pruned 19023 variants from chromosome 3, leaving 6118.
##
0%
1%
2%
3%
4%
5%
6%
7%
7%
8%
8%
9%
10%
11%
12%
13%
14%
15%
15%
16%
16%
17%
18%
19%
20%
21%
22%
23%
23%
24%
24%
25%
26%
27%
28%
29%
30%
31%
31%
32%
32%
33%
34%
35%
36%
37%
38%
39%
39%
40%
40%
41%
42%
43%
44%
45%
46%
47%
47%
48%
48%
49%
50%
51%
52%
53%
54%
55%
55%
56%
56%
57%
58%
59%
60%
61%
62%
63%
63%
64%
64%
65%
66%
67%
68%
69%
70%
71%
71%
72%
72%
73%
74%
75%
76%
77%
78%
79%
79%
80%
81%
82%
83%
84%
85%
86%
87%
87%
88%
89%
90%
91%
92%
93%
94%
95%
95%
96%
97%
98%
99%
Pruned 18135 variants from chromosome 4, leaving 5928.
##
1%
2%
3%
4%
5%
6%
7%
8%
8%
9%
10%
11%
12%
12%
13%
14%
15%
16%
16%
17%
18%
19%
20%
20%
21%
22%
23%
24%
24%
25%
26%
27%
28%
29%
30%
31%
32%
32%
33%
34%
35%
36%
36%
37%
38%
39%
40%
40%
41%
42%
43%
44%
44%
45%
46%
47%
48%
48%
49%
50%
51%
52%
52%
53%
54%
55%
56%
57%
58%
59%
60%
61%
62%
63%
64%
65%
65%
66%
67%
68%
69%
70%
71%
72%
72%
73%
74%
75%
76%
76%
77%
78%
79%
80%
80%
81%
82%
83%
84%
85%
86%
87%
88%
89%
89%
90%
91%
92%
93%
93%
94%
95%
96%
97%
97%
98%
99%
Pruned 18263 variants from chromosome 5, leaving 5915.
##
1%
2%
3%
4%
4%
5%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
14%
15%
16%
17%
18%
25%
26%
27%
28%
28%
29%
30%
31%
32%
33%
33%
34%
35%
36%
37%
38%
38%
39%
40%
41%
42%
42%
43%
44%
45%
46%
47%
47%
48%
49%
50%
51%
52%
52%
53%
54%
55%
56%
57%
57%
58%
59%
60%
61%
62%
62%
63%
64%
65%
66%
67%
67%
68%
69%
70%
71%
72%
72%
73%
74%
75%
76%
77%
77%
78%
79%
80%
81%
82%
83%
84%
85%
85%
86%
87%
88%
89%
90%
90%
91%
92%
93%
94%
95%
95%
96%
97%
98%
99%
Pruned 16939 variants from chromosome 6, leaving 5428.
##
1%
2%
2%
3%
4%
5%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
15%
16%
16%
17%
18%
19%
20%
21%
22%
23%
23%
24%
25%
26%
27%
28%
29%
30%
30%
31%
32%
33%
34%
35%
36%
37%
37%
38%
39%
40%
41%
42%
43%
44%
46%
47%
48%
49%
49%
50%
51%
52%
53%
54%
55%
56%
56%
57%
58%
59%
60%
61%
62%
63%
63%
64%
65%
66%
67%
68%
69%
70%
70%
71%
72%
73%
74%
75%
76%
77%
77%
78%
79%
80%
81%
82%
83%
84%
84%
85%
86%
87%
88%
89%
90%
91%
91%
92%
93%
94%
95%
96%
97%
98%
98%
99%
Pruned 14398 variants from chromosome 7, leaving 5006.
##
1%
2%
3%
4%
5%
6%
7%
8%
9%
13%
14%
15%
16%
17%
18%
19%
20%
21%
21%
22%
22%
23%
23%
24%
25%
26%
27%
28%
29%
30%
31%
32%
33%
34%
35%
36%
37%
38%
39%
40%
41%
42%
43%
43%
44%
44%
45%
45%
46%
47%
48%
49%
50%
51%
52%
53%
54%
55%
56%
57%
58%
59%
59%
60%
60%
61%
61%
62%
63%
64%
65%
66%
67%
68%
69%
70%
71%
72%
73%
74%
75%
76%
77%
78%
78%
79%
79%
80%
80%
81%
82%
83%
84%
85%
86%
87%
88%
89%
90%
91%
92%
93%
93%
94%
94%
95%
95%
96%
97%
98%
99%
Pruned 15060 variants from chromosome 8, leaving 4619.
##
1%
2%
3%
4%
5%
6%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
15%
16%
17%
18%
19%
19%
20%
21%
22%
22%
23%
24%
25%
26%
27%
28%
29%
29%
30%
31%
32%
32%
33%
34%
35%
35%
36%
37%
38%
39%
40%
41%
42%
42%
43%
44%
45%
45%
46%
47%
48%
49%
50%
51%
52%
53%
54%
55%
55%
56%
57%
58%
58%
59%
60%
61%
62%
63%
64%
65%
65%
66%
67%
68%
68%
69%
70%
71%
71%
72%
73%
74%
75%
76%
77%
78%
78%
79%
80%
81%
81%
82%
83%
84%
84%
85%
86%
87%
88%
89%
90%
91%
91%
92%
93%
94%
94%
95%
96%
97%
98%
99%
Pruned 13214 variants from chromosome 9, leaving 4439.
##
1%
2%
3%
4%
5%
5%
6%
7%
8%
9%
10%
11%
12%
12%
13%
14%
15%
16%
17%
18%
19%
19%
20%
21%
22%
23%
24%
25%
26%
26%
27%
28%
29%
30%
31%
33%
34%
34%
35%
35%
36%
37%
38%
39%
40%
41%
41%
42%
42%
43%
44%
45%
46%
47%
48%
48%
49%
50%
51%
52%
53%
54%
55%
55%
56%
57%
58%
59%
60%
61%
62%
62%
63%
64%
65%
66%
67%
68%
69%
69%
70%
71%
72%
73%
74%
75%
76%
76%
77%
78%
79%
80%
81%
82%
83%
83%
84%
85%
86%
87%
88%
89%
90%
90%
91%
92%
93%
94%
95%
96%
97%
97%
98%
99%
Pruned 16391 variants from chromosome 10, leaving 5108.
##
1%
2%
3%
4%
5%
6%
7%
8%
9%
10%
11%
12%
13%
14%
15%
16%
17%
18%
19%
20%
21%
22%
23%
24%
25%
26%
27%
28%
29%
30%
31%
32%
33%
34%
35%
36%
37%
38%
39%
40%
41%
42%
43%
44%
45%
46%
47%
48%
49%
50%
51%
52%
53%
54%
55%
56%
57%
58%
59%
60%
62%
63%
64%
64%
65%
66%
67%
67%
68%
69%
70%
70%
71%
72%
73%
73%
74%
75%
76%
76%
77%
78%
79%
79%
80%
81%
82%
82%
83%
84%
85%
85%
86%
87%
88%
88%
89%
90%
91%
91%
92%
93%
94%
94%
95%
96%
97%
97%
98%
99%
Pruned 14918 variants from chromosome 11, leaving 4584.
##
1%
2%
2%
3%
4%
5%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
15%
16%
16%
17%
18%
19%
20%
21%
22%
23%
23%
24%
25%
26%
27%
32%
33%
33%
34%
35%
36%
36%
37%
38%
39%
40%
41%
42%
43%
43%
44%
45%
46%
47%
48%
49%
50%
50%
51%
52%
53%
54%
55%
56%
57%
57%
58%
59%
60%
61%
62%
63%
64%
64%
65%
66%
67%
68%
69%
70%
71%
71%
72%
73%
74%
75%
76%
77%
78%
78%
79%
80%
81%
81%
82%
83%
84%
85%
85%
86%
87%
88%
88%
89%
90%
91%
92%
92%
93%
94%
95%
95%
96%
97%
98%
99%
Pruned 13334 variants from chromosome 12, leaving 4661.
##
1%
2%
3%
4%
4%
5%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
15%
15%
16%
17%
18%
19%
20%
20%
21%
22%
23%
24%
25%
26%
26%
27%
28%
29%
30%
31%
31%
32%
33%
34%
35%
36%
37%
37%
38%
39%
40%
41%
42%
42%
43%
44%
45%
46%
47%
48%
48%
49%
50%
51%
52%
53%
53%
54%
55%
56%
57%
58%
59%
59%
60%
61%
62%
63%
64%
64%
65%
66%
67%
68%
69%
70%
70%
71%
72%
73%
74%
75%
75%
76%
77%
78%
79%
80%
81%
81%
82%
83%
84%
85%
86%
86%
87%
88%
89%
90%
91%
92%
92%
93%
94%
95%
96%
97%
97%
98%
99%
Pruned 10794 variants from chromosome 13, leaving 3615.
##
1%
2%
2%
3%
4%
5%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
15%
16%
16%
17%
18%
19%
19%
20%
21%
22%
23%
24%
25%
26%
26%
27%
28%
29%
30%
31%
32%
33%
33%
34%
35%
36%
36%
37%
38%
39%
40%
40%
41%
42%
43%
43%
44%
45%
46%
47%
48%
49%
50%
50%
51%
52%
53%
54%
55%
56%
57%
57%
58%
59%
60%
60%
61%
62%
63%
64%
64%
65%
66%
67%
67%
68%
69%
70%
71%
72%
73%
74%
74%
75%
76%
77%
78%
79%
80%
81%
81%
82%
83%
84%
84%
85%
86%
87%
88%
88%
89%
90%
91%
91%
92%
93%
94%
95%
96%
97%
98%
98%
99%
Pruned 8697 variants from chromosome 14, leaving 3157.
##
1%
1%
2%
3%
3%
4%
5%
5%
6%
7%
7%
8%
9%
9%
10%
11%
11%
12%
13%
13%
14%
15%
15%
16%
17%
17%
18%
19%
19%
20%
21%
21%
22%
23%
23%
24%
25%
25%
26%
27%
27%
28%
29%
29%
30%
31%
31%
32%
33%
33%
34%
35%
35%
36%
37%
37%
38%
39%
39%
40%
41%
41%
42%
43%
43%
44%
45%
45%
46%
47%
47%
48%
49%
50%
51%
52%
53%
54%
55%
56%
57%
58%
59%
60%
61%
62%
63%
64%
65%
66%
67%
68%
69%
70%
71%
72%
73%
74%
75%
76%
77%
78%
79%
80%
81%
82%
83%
84%
85%
86%
87%
88%
89%
90%
91%
92%
93%
94%
95%
96%
97%
98%
99%
Pruned 7689 variants from chromosome 15, leaving 3063.
##
1%
2%
2%
3%
4%
5%
5%
6%
7%
8%
9%
10%
10%
11%
12%
13%
13%
14%
15%
16%
17%
18%
19%
20%
21%
21%
22%
23%
24%
24%
25%
26%
27%
28%
29%
30%
31%
32%
32%
33%
34%
35%
35%
36%
37%
38%
39%
40%
40%
41%
42%
43%
43%
44%
45%
46%
47%
48%
49%
50%
51%
51%
52%
53%
54%
54%
55%
56%
57%
58%
59%
60%
61%
62%
62%
63%
64%
65%
65%
66%
67%
68%
69%
70%
71%
72%
73%
73%
74%
75%
76%
76%
77%
78%
79%
80%
81%
81%
82%
83%
84%
84%
85%
86%
87%
88%
89%
90%
91%
92%
92%
93%
94%
95%
95%
96%
97%
98%
99%
Pruned 8445 variants from chromosome 16, leaving 3238.
##
1%
2%
3%
4%
5%
6%
6%
7%
8%
9%
9%
10%
11%
12%
12%
13%
14%
15%
15%
16%
17%
18%
19%
20%
21%
22%
23%
24%
25%
25%
26%
27%
28%
28%
29%
30%
31%
31%
32%
33%
34%
35%
36%
37%
38%
39%
40%
41%
41%
42%
43%
44%
44%
45%
46%
47%
47%
48%
49%
50%
50%
51%
52%
53%
54%
55%
56%
57%
58%
59%
60%
60%
61%
62%
63%
63%
64%
65%
66%
66%
67%
68%
69%
70%
71%
72%
73%
74%
75%
76%
76%
77%
78%
79%
79%
80%
81%
82%
82%
83%
84%
85%
85%
86%
87%
88%
89%
90%
91%
92%
93%
94%
95%
95%
96%
97%
98%
98%
99%
Pruned 5918 variants from chromosome 17, leaving 2739.
##
1%
2%
3%
3%
4%
5%
6%
7%
7%
8%
9%
10%
11%
11%
12%
13%
14%
15%
16%
17%
18%
18%
19%
20%
21%
22%
22%
23%
24%
25%
26%
26%
27%
28%
29%
30%
31%
32%
33%
33%
34%
35%
36%
37%
37%
38%
39%
40%
41%
41%
42%
43%
44%
45%
46%
47%
48%
48%
49%
50%
51%
52%
52%
53%
54%
55%
56%
56%
57%
58%
59%
60%
61%
62%
63%
63%
64%
65%
66%
67%
67%
68%
69%
70%
71%
71%
72%
73%
74%
75%
76%
77%
78%
78%
79%
80%
81%
82%
82%
83%
84%
85%
86%
86%
87%
88%
89%
90%
91%
92%
93%
93%
94%
95%
96%
97%
97%
98%
99%
Pruned 8099 variants from chromosome 18, leaving 3034.
##
1%
2%
3%
4%
5%
6%
7%
8%
9%
10%
10%
11%
11%
12%
13%
14%
15%
16%
17%
18%
19%
20%
21%
22%
22%
23%
23%
24%
25%
26%
27%
28%
29%
30%
31%
32%
33%
34%
35%
35%
36%
36%
37%
38%
39%
40%
41%
42%
43%
44%
45%
46%
47%
47%
48%
48%
49%
50%
51%
52%
53%
54%
55%
56%
57%
58%
59%
60%
60%
61%
61%
62%
63%
64%
65%
66%
67%
68%
69%
70%
71%
72%
72%
73%
73%
74%
75%
76%
77%
78%
79%
80%
81%
82%
83%
84%
85%
85%
86%
86%
87%
88%
89%
90%
91%
92%
93%
94%
95%
96%
97%
97%
98%
98%
99%
Pruned 3156 variants from chromosome 19, leaving 1804.
##
1%
2%
3%
4%
5%
6%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
15%
16%
16%
17%
18%
19%
19%
20%
21%
22%
23%
24%
25%
26%
27%
28%
29%
29%
30%
31%
32%
32%
33%
34%
35%
36%
37%
38%
39%
39%
40%
41%
42%
42%
43%
44%
45%
46%
47%
48%
49%
50%
51%
52%
54%
54%
55%
56%
57%
57%
58%
59%
60%
61%
62%
63%
64%
64%
65%
66%
67%
67%
68%
69%
70%
71%
72%
73%
74%
75%
76%
77%
77%
78%
79%
80%
80%
81%
82%
83%
84%
85%
86%
87%
87%
88%
89%
90%
90%
91%
92%
93%
94%
95%
96%
97%
97%
98%
99%
Pruned 6826 variants from chromosome 20, leaving 2638.
##
1%
2%
3%
4%
4%
5%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
14%
15%
16%
17%
18%
19%
19%
20%
21%
22%
23%
24%
24%
25%
26%
27%
28%
29%
29%
30%
31%
32%
33%
34%
35%
35%
36%
37%
38%
39%
40%
40%
41%
42%
43%
44%
45%
45%
46%
47%
48%
49%
50%
50%
51%
52%
53%
54%
55%
55%
56%
57%
58%
59%
60%
60%
61%
62%
63%
64%
65%
65%
66%
66%
67%
68%
69%
70%
71%
71%
72%
73%
74%
75%
76%
76%
77%
78%
79%
80%
81%
81%
82%
83%
84%
85%
86%
86%
87%
88%
89%
90%
91%
91%
92%
93%
94%
95%
96%
96%
97%
98%
99%
Pruned 3902 variants from chromosome 21, leaving 1501.
##
1%
1%
2%
3%
4%
5%
6%
6%
7%
8%
9%
10%
11%
11%
12%
13%
14%
15%
16%
16%
17%
18%
19%
20%
21%
22%
23%
23%
24%
25%
26%
27%
28%
28%
29%
30%
31%
32%
33%
33%
34%
35%
36%
37%
38%
38%
39%
40%
40%
41%
42%
43%
44%
45%
45%
46%
47%
48%
49%
50%
50%
51%
52%
53%
54%
55%
55%
56%
57%
58%
59%
60%
61%
62%
62%
63%
64%
65%
66%
67%
67%
68%
69%
70%
71%
72%
72%
73%
74%
75%
76%
77%
77%
78%
79%
80%
81%
82%
83%
84%
84%
85%
86%
87%
88%
89%
89%
90%
91%
92%
93%
94%
94%
95%
96%
97%
98%
99%
Pruned 3299 variants from chromosome 22, leaving 1496.
##
1%
2%
3%
4%
4%
5%
6%
7%
8%
9%
9%
10%
11%
12%
13%
14%
14%
15%
16%
17%
18%
19%
19%
20%
21%
22%
23%
24%
25%
25%
26%
27%
28%
29%
30%
30%
31%
32%
33%
34%
35%
35%
36%
37%
38%
39%
40%
40%
41%
42%
43%
44%
45%
45%
46%
47%
48%
49%
50%
51%
51%
52%
53%
54%
55%
56%
56%
57%
58%
59%
60%
61%
61%
62%
63%
64%
65%
66%
66%
67%
68%
69%
70%
71%
71%
72%
73%
74%
75%
76%
77%
77%
78%
79%
80%
81%
82%
82%
83%
84%
85%
86%
87%
87%
88%
89%
90%
91%
92%
92%
93%
94%
95%
96%
97%
97%
98%
99%
Pruned 5703 variants from chromosome 23, leaving 2201.
##
2%
5%
8%
11%
14%
17%
20%
23%
26%
29%
32%
35%
38%
41%
44%
47%
50%
53%
56%
59%
62%
65%
68%
71%
73%
76%
79%
82%
85%
88%
91%
94%
97%
Pruned 54 variants from chromosome 25, leaving 115.
## Pruning complete. 276925 of 372059 variants removed.
## Writing...
Marker lists written to
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.prune.in
## and
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.prune.out
## .
## PLINK v1.90b6.26 64-bit (2 Apr 2022) www.cog-genomics.org/plink/1.9/
## (C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3
## Logging to C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.log.
## Options in effect:
## --bfile C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas
## --extract C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.prune.in
## --genome
## --maf 0.1
## --out C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas
##
## 15775 MB RAM detected; reserving 7887 MB for main workspace.
## 380157 variants loaded from .bim file.
## 364 people (191 males, 173 females) loaded from .fam.
## 364 phenotype values loaded from .fam.
## --extract: 95134 variants remaining.
## Using up to 15 threads (change this with --threads).
## Before main variant filters, 364 founders and 0 nonfounders present.
## Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
## Total genotyping rate is 0.970469.
## 35068 variants removed due to minor allele threshold(s)
## (--maf/--max-maf/--mac/--max-mac).
## 60066 variants and 364 people pass filters and QC.
## Among remaining phenotypes, 176 are cases and 188 are controls.
## Excluding 1410 variants on non-autosomes from IBD calculation.
##
1152 markers complete.
2304 markers complete.
3456 markers complete.
4608 markers complete.
5760 markers complete.
6912 markers complete.
8064 markers complete.
9216 markers complete.
10368 markers complete.
11520 markers complete.
12672 markers complete.
13824 markers complete.
14976 markers complete.
16128 markers complete.
17280 markers complete.
18432 markers complete.
19584 markers complete.
20736 markers complete.
21888 markers complete.
23040 markers complete.
24192 markers complete.
25344 markers complete.
26496 markers complete.
27648 markers complete.
28800 markers complete.
29952 markers complete.
31104 markers complete.
32256 markers complete.
33408 markers complete.
34560 markers complete.
35712 markers complete.
36864 markers complete.
38016 markers complete.
39168 markers complete.
40320 markers complete.
41472 markers complete.
42624 markers complete.
43776 markers complete.
44928 markers complete.
46080 markers complete.
47232 markers complete.
48384 markers complete.
49536 markers complete.
50688 markers complete.
51840 markers complete.
52992 markers complete.
54144 markers complete.
55296 markers complete.
56448 markers complete.
57600 markers complete.
58656 markers complete.
IBD calculations complete.
##
Writing... 1%
Writing... 3%
Writing... 5%
Writing... 8%
Writing... 10%
Writing... 12%
Writing... 14%
Writing... 16%
Writing... 18%
Writing... 20%
Writing... 22%
Writing... 25%
Writing... 27%
Writing... 29%
Writing... 31%
Writing... 33%
Writing... 35%
Writing... 37%
Writing... 40%
Writing... 42%
Writing... 44%
Writing... 46%
Writing... 48%
Writing... 50%
Writing... 52%
Writing... 54%
Writing... 56%
Writing... 59%
Writing... 61%
Writing... 63%
Writing... 65%
Writing... 67%
Writing... 69%
Writing... 71%
Writing... 73%
Writing... 75%
Writing... 77%
Writing... 80%
Writing... 82%
Writing... 84%
Writing... 86%
Writing... 88%
Writing... 90%
Writing... 92%
Writing... 94%
Writing... 97%
Writing... 99%
Finished writing
## C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.genome
## .
First perIndividual QC
fail_individuals <- perIndividualQC(indir=indir, qcdir=qcdir, name=name, path2plink=path2plink,
dont.check_sex=TRUE, dont.check_ancestry=TRUE,
imissTh = 0.1, hetTh = 3,
highIBDTh=0.2,
interactive=TRUE, verbose=TRUE, showPlinkOutput=FALSE)## Run check_missingness via plink --missing## Run check_heterozygosity via plink --het## Identification of individuals with outlying missing genotype or heterozygosity rates## Use hg19 coordinates for pruning of high-ld regions## Prune C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas for relatedness estimation## Run check_relatedness via plink --genome## Identification of related individuals## Combine fail IDs into C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/output/binary_adgwas.fail.IDs
Can also check for SNP missingness
fail_snpmissing <- check_snp_missingness(indir, name, qcdir=indir, path2plink=path2plink,
lmissTh = 0.01,
interactive=TRUE, showPlinkOutput=FALSE)## File with individuals that failed perIndividualQC: C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas.fail.IDs does not exist. Continue check_SNP_missingness for all samples in C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas.fam
##Check HWE
check_hwe(indir, name, qcdir=indir, path2plink=path2plink,
hweTh = 1e-05,
interactive=TRUE, verbose=TRUE, showPlinkOutput=FALSE)## File with individuals that failed perIndividualQC: C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas.fail.IDs does not exist. Continue check_HWE for all samples in C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas.fam
## $fail_hwe
## CHR SNP TEST A1 A2 GENO O.HET. E.HET. P
## 5539 1 rs1056207 ALL T C 13/46/279 0.136100 0.19030 5.333e-06
## 10975 1 rs17342387 ALL C T 6/15/317 0.044380 0.07669 8.905e-07
## 15025 1 rs12024669 ALL C T 31/84/218 0.252300 0.34230 3.061e-06
## 19678 1 rs1331853 ALL T G 36/216/89 0.633400 0.48790 3.192e-08
## 21265 1 rs338945 ALL G C 13/181/161 0.509900 0.41310 4.106e-06
## 23785 1 rs285360 ALL G A 29/74/234 0.219600 0.31500 2.209e-07
## 27025 1 rs12116755 ALL C T 12/36/294 0.105300 0.16000 2.883e-07
## 28645 1 rs12123977 ALL A G 10/171/159 0.502900 0.40400 2.671e-06
## 29527 1 rs17100274 ALL C T 6/18/328 0.051140 0.08160 3.309e-06
## 29614 1 rs6695572 ALL T C 24/60/257 0.176000 0.26660 1.061e-08
## 31561 1 rs785601 ALL C A 10/168/168 0.485500 0.39570 8.223e-06
## 46723 1 rs942835 ALL G A 23/70/244 0.207700 0.28500 2.503e-06
## 46822 1 rs2453044 ALL G A 18/57/279 0.161000 0.22820 6.794e-07
## 49084 1 rs348184 ALL G A 1/142/169 0.455100 0.35500 9.952e-09
## 49750 1 rs2758674 ALL C T 6/152/175 0.456500 0.37120 9.467e-06
## 56656 1 rs10800570 ALL G T 20/67/253 0.197100 0.26520 8.496e-06
## 59926 1 rs3766637 ALL C T 8/28/293 0.085110 0.12480 8.247e-06
## 65890 1 rs615747 ALL T A 10/33/300 0.096210 0.14260 1.690e-06
## 66598 1 rs2094028 ALL A G 25/80/256 0.221600 0.29530 6.141e-06
## 66700 1 rs800290 ALL G A 15/184/143 0.538000 0.43000 1.887e-06
## 70558 1 rs823066 ALL A G 9/32/309 0.091430 0.13270 4.730e-06
## 73417 1 rs7518399 ALL G C 1/136/217 0.384200 0.31380 1.396e-06
## 81343 1 rs2296799 ALL G A 26/76/238 0.223500 0.30560 2.438e-06
## 81937 1 rs12029109 ALL C T 7/25/318 0.071430 0.10520 9.474e-06
## 82291 1 rs4649265 ALL C A 6/14/338 0.039110 0.06999 3.568e-07
## 83707 1 rs982900 ALL A G 8/24/311 0.069970 0.10980 1.026e-06
## 87778 1 rs10926940 ALL T C 13/189/148 0.540000 0.42560 1.337e-07
## 95533 2 rs6432150 ALL C A 18/62/259 0.182900 0.24730 8.838e-06
## 111655 2 rs10167668 ALL G A 13/48/281 0.140400 0.19300 9.744e-06
## 111925 2 rs4952782 ALL A T 2/138/197 0.409500 0.33260 1.630e-06
## 112390 2 rs2121700 ALL C A 80/117/124 0.364500 0.49060 3.736e-06
## 117274 2 rs17189361 ALL G T 69/112/149 0.339400 0.47060 3.136e-07
## 119263 2 rs4233978 ALL G A 25/77/242 0.223800 0.30100 5.513e-06
## 124063 2 rs608112 ALL A G 5/157/186 0.451100 0.36470 2.298e-06
## 131515 2 rs17027293 ALL G A 11/39/290 0.114700 0.16330 4.719e-06
## 136447 2 rs4848411 ALL G C 71/127/156 0.358800 0.47120 7.586e-06
## 142570 2 rs16837705 ALL C T 21/66/249 0.196400 0.26980 3.056e-06
## 149569 2 rs13005519 ALL C T 5/10/340 0.028170 0.05475 4.800e-07
## 155782 2 rs16823058 ALL C T 15/23/311 0.065900 0.14030 4.181e-13
## 157828 2 rs2646165 ALL G A 18/62/259 0.182900 0.24730 8.838e-06
## 160444 2 rs2292855 ALL C T 6/11/327 0.031980 0.06463 6.585e-08
## 160534 2 rs6728366 ALL T G 57/109/158 0.336400 0.45140 6.100e-06
## 160978 2 rs10497601 ALL T C 31/84/223 0.248500 0.33870 2.454e-06
## 186715 3 rs4635693 ALL G A 25/76/247 0.218400 0.29650 3.602e-06
## 186979 3 rs2090350 ALL T C 23/200/123 0.578000 0.45820 9.365e-07
## 187279 3 rs17044542 ALL C A 14/30/279 0.092880 0.16340 1.013e-09
## 192580 3 rs6442561 ALL C T 22/57/261 0.167600 0.25290 2.036e-08
## 196513 3 rs1681549 ALL A G 59/113/181 0.320100 0.44030 3.949e-07
## 196750 3 rs17593351 ALL C T 29/81/213 0.250800 0.33770 7.496e-06
## 196813 3 rs1548008 ALL G A 11/37/300 0.106300 0.15520 1.669e-06
## 197365 3 rs6799404 ALL G T 13/47/288 0.135100 0.18780 5.525e-06
## 198562 3 rs12715170 ALL T C 65/114/147 0.349700 0.46840 4.677e-06
## 201574 3 rs17828003 ALL G A 7/24/310 0.070380 0.10520 7.440e-06
## 205732 3 rs201198 ALL C T 16/57/267 0.167600 0.22750 9.865e-06
## 212689 3 rs17071854 ALL C T 15/55/283 0.155800 0.21180 8.361e-06
## 212713 3 rs11708001 ALL C A 5/154/200 0.429000 0.35250 7.276e-06
## 217693 3 rs7612336 ALL C T 4/7/334 0.020290 0.04253 1.497e-06
## 219823 3 rs1968814 ALL T C 34/90/224 0.258600 0.35100 1.859e-06
## 224422 3 rs1440784 ALL T G 6/19/329 0.053670 0.08374 5.123e-06
## 239239 3 rs6787459 ALL G A 0/118/231 0.338100 0.28100 7.696e-06
## 241954 3 rs1350226 ALL T A 26/78/235 0.230100 0.31000 8.874e-06
## 248263 3 rs4680661 ALL C T 6/20/328 0.056500 0.08631 8.034e-06
## 248719 3 rs6776030 ALL C A 7/162/167 0.482100 0.38660 1.503e-06
## 250339 3 rs13099331 ALL T C 15/50/294 0.139300 0.19800 1.028e-06
## 253483 3 rs6778471 ALL G A 63/117/156 0.348200 0.46170 8.429e-06
## 254362 3 rs7612178 ALL A C 23/73/259 0.205600 0.27900 2.866e-06
## 258370 3 rs6444705 ALL C T 8/18/316 0.052630 0.09447 4.271e-08
## 263617 4 rs13102699 ALL G A 0/119/218 0.353100 0.29080 4.227e-06
## 266386 4 rs10017117 ALL C T 13/27/295 0.080600 0.14570 5.582e-10
## 268561 4 rs531823 ALL C A 81/124/146 0.353300 0.48290 4.266e-07
## 271756 4 rs10016498 ALL T C 34/205/107 0.592500 0.47770 8.084e-06
## 281524 4 rs7699089 ALL G A 15/54/275 0.157000 0.21440 8.195e-06
## 283720 4 rs9884270 ALL C T 13/46/274 0.138100 0.19280 6.343e-06
## 283780 4 rs6554508 ALL G T 15/47/278 0.138200 0.20080 6.303e-07
## 293845 4 rs17364803 ALL C T 13/47/275 0.140300 0.19420 8.589e-06
## 294445 4 rs11097084 ALL G A 32/82/210 0.253100 0.34910 1.501e-06
## 294652 4 rs12171459 ALL C T 15/41/276 0.123500 0.19100 5.862e-08
## 298777 4 rs6823388 ALL A G 8/21/334 0.057850 0.09673 1.460e-07
## 303172 4 rs6827443 ALL A G 24/195/100 0.611300 0.47160 9.994e-08
## 304864 4 rs2174668 ALL G A 22/70/253 0.202900 0.27580 3.657e-06
## 306601 4 rs994831 ALL G A 8/26/317 0.074070 0.11250 2.145e-06
## 312376 4 rs17050680 ALL C T 52/108/173 0.324300 0.43400 6.168e-06
## 315193 4 rs1979957 ALL C G 77/122/140 0.359900 0.48270 2.724e-06
## 315691 4 rs10021848 ALL G C 6/161/186 0.456100 0.37000 4.012e-06
## 317419 4 rs3804100 ALL G A 9/34/309 0.096590 0.13680 9.827e-06
## 319504 4 rs17037858 ALL C T 4/6/334 0.017440 0.03987 7.108e-07
## 329668 4 rs1217973 ALL C A 15/53/269 0.157300 0.21600 7.461e-06
## 339097 5 rs852585 ALL T G 7/19/311 0.056380 0.09313 7.723e-07
## 339139 5 rs7730123 ALL G A 8/27/300 0.080600 0.12010 4.732e-06
## 343795 5 rs6859281 ALL C T 5/13/338 0.036520 0.06252 2.839e-06
## 354736 5 rs16886496 ALL C T 10/31/303 0.090120 0.13730 6.841e-07
## 355492 5 rs11953112 ALL A C 32/82/214 0.250000 0.34610 1.242e-06
## 357592 5 rs1176261 ALL C T 10/177/156 0.516000 0.40940 5.156e-07
## 359584 5 rs382480 ALL G A 73/108/145 0.331300 0.47560 4.761e-08
## 359716 5 rs625637 ALL A C 4/162/183 0.464200 0.36850 1.185e-07
## 364009 5 rs256447 ALL C T 28/69/240 0.204700 0.30210 2.693e-08
## 367591 5 rs17640214 ALL G A 35/70/221 0.214700 0.33720 4.217e-10
## 368005 5 rs10036284 ALL G A 7/19/309 0.056720 0.09366 8.045e-07
## 377116 5 rs3097167 ALL C T 23/72/242 0.213600 0.28880 9.035e-06
## 378994 5 rs17147703 ALL G T 15/48/278 0.140800 0.20260 9.178e-07
## 380134 5 rs6595509 ALL T A 28/209/94 0.631400 0.48010 5.584e-09
## 384943 5 rs6596271 ALL C T 9/29/299 0.086050 0.12970 1.852e-06
## 403423 5 rs2913481 ALL A G 33/219/94 0.632900 0.48450 8.479e-09
## 405823 5 rs2546437 ALL C T 11/38/290 0.112100 0.16130 3.274e-06
## 417547 6 rs16884319 ALL G T 5/14/333 0.039770 0.06586 5.082e-06
## 418000 6 rs196026 ALL A C 46/224/74 0.651200 0.49670 9.999e-09
## 421120 6 rs9257461 ALL A G 91/127/118 0.378000 0.49680 8.444e-06
## 421801 6 rs439935 ALL G C 21/58/263 0.169600 0.24960 8.121e-08
## 423724 6 rs3957146 ALL C T 15/53/279 0.152700 0.21060 5.086e-06
## 424291 6 rs210138 ALL C T 25/72/237 0.215600 0.29860 2.560e-06
## 437122 6 rs9346051 ALL G A 8/26/325 0.072420 0.11010 1.803e-06
## 437350 6 rs2603687 ALL C T 32/76/211 0.238200 0.34260 2.131e-07
## 440485 6 rs6908385 ALL A G 20/65/248 0.195200 0.26560 5.821e-06
## 442045 6 rs2603457 ALL C T 28/76/230 0.227500 0.31710 8.070e-07
## 446575 6 rs6454872 ALL C A 53/109/172 0.326300 0.43650 4.004e-06
## 452491 6 rs1913 ALL G A 6/163/169 0.482200 0.38370 3.054e-07
## 454087 6 rs9481246 ALL A G 25/206/105 0.613100 0.47170 2.986e-08
## 458545 6 rs2753181 ALL C T 32/90/224 0.260100 0.34600 6.515e-06
## 459394 6 rs9385404 ALL C T 37/82/209 0.250000 0.36250 5.528e-08
## 459424 6 rs1361831 ALL C T 105/133/113 0.378900 0.49970 5.330e-06
## 461680 6 rs9399023 ALL C A 10/37/305 0.105100 0.14880 6.639e-06
## 463009 6 rs9402750 ALL C A 8/28/314 0.080000 0.11780 5.150e-06
## 470494 6 rs1892355 ALL C T 58/102/170 0.309100 0.44240 4.395e-08
## 470719 6 rs599945 ALL C A 11/35/305 0.099720 0.14920 6.529e-07
## 475855 6 rs794099 ALL C T 6/19/332 0.053220 0.08306 4.876e-06
## 481057 7 rs1474445 ALL G A 28/73/230 0.220500 0.31380 4.149e-07
## 482059 7 rs17143355 ALL G A 19/58/241 0.182400 0.25630 2.094e-06
## 488632 7 rs2965396 ALL C T 6/16/336 0.044690 0.07515 1.091e-06
## 503485 7 rs9791781 ALL C A 7/10/326 0.029150 0.06752 1.893e-09
## 504871 7 rs12533567 ALL G A 10/36/286 0.108400 0.15440 7.762e-06
## 507385 7 rs4318930 ALL T A 23/202/118 0.588900 0.46160 1.611e-07
## 508285 7 rs6958850 ALL C T 12/31/288 0.093660 0.15240 3.638e-08
## 512086 7 rs10261664 ALL C T 22/68/255 0.197100 0.27190 1.719e-06
## 519808 7 rs2237649 ALL C T 108/132/113 0.373900 0.49990 2.011e-06
## 522961 7 rs10241082 ALL G A 24/68/243 0.203000 0.28630 5.578e-07
## 525394 7 rs12113012 ALL G A 7/24/317 0.068970 0.10320 6.488e-06
## 525580 7 rs1419585 ALL C T 59/113/157 0.343500 0.45560 8.785e-06
## 526900 7 rs879003 ALL T C 24/72/240 0.214300 0.29340 4.787e-06
## 528502 7 rs985101 ALL A T 20/48/269 0.142400 0.22700 2.545e-09
## 529885 7 rs1364746 ALL A T 43/88/202 0.264300 0.38600 1.951e-08
## 530143 7 rs11978828 ALL C T 32/67/223 0.208100 0.32410 1.247e-09
## 534766 7 rs354075 ALL A G 12/170/153 0.507500 0.41140 7.347e-06
## 536764 7 rs3778738 ALL C T 14/46/279 0.135700 0.19450 1.494e-06
## 539056 8 rs2701907 ALL G A 52/104/171 0.318000 0.43380 1.413e-06
## 539815 8 rs2607684 ALL G T 5/167/174 0.482700 0.38070 5.830e-08
## 548686 8 rs17120794 ALL C T 9/33/307 0.094560 0.13550 7.195e-06
## 552811 8 rs2610943 ALL C T 31/86/230 0.247800 0.33560 2.727e-06
## 556678 8 rs17059008 ALL C T 11/32/296 0.094400 0.14660 2.394e-07
## 568729 8 rs6982872 ALL G A 20/62/267 0.177700 0.24960 8.297e-07
## 574618 8 rs6986945 ALL C A 24/74/232 0.224200 0.30140 8.761e-06
## 575473 8 rs6981188 ALL G A 93/124/121 0.366900 0.49660 1.044e-06
## 578194 8 rs843094 ALL C T 38/97/202 0.287800 0.38160 9.805e-06
## 579004 8 rs2446834 ALL T C 9/13/319 0.038120 0.08678 1.141e-10
## 585775 8 rs10108155 ALL G A 33/87/208 0.265200 0.35770 6.824e-06
## 595174 8 rs4388439 ALL C T 9/26/311 0.075140 0.11910 3.684e-07
## 599152 8 rs16908893 ALL G A 4/4/353 0.011080 0.03269 9.729e-08
## 602005 9 rs16923301 ALL A G 8/18/332 0.050280 0.09046 2.975e-08
## 602695 9 rs12339146 ALL C A 18/64/271 0.181300 0.24320 9.682e-06
## 605794 9 rs10975413 ALL G A 27/80/227 0.239500 0.32070 7.934e-06
## 608512 9 rs7851330 ALL C T 8/29/308 0.084060 0.12190 8.620e-06
## 613915 9 rs457062 ALL C T 11/29/307 0.083570 0.13620 4.220e-08
## 614257 9 rs12057044 ALL C T 49/100/186 0.298500 0.41640 2.945e-07
## 620695 9 rs1622785 ALL T C 14/175/145 0.524000 0.42310 6.665e-06
## 634354 9 rs16908281 ALL G C 6/19/321 0.054910 0.08558 5.858e-06
## 639478 9 rs7866945 ALL G A 28/68/238 0.203600 0.30230 2.090e-08
## 649807 9 rs12236873 ALL C T 3/144/193 0.423500 0.34390 1.961e-06
## 650857 9 rs4083644 ALL A G 9/164/170 0.478100 0.38980 9.965e-06
## 655102 10 rs10508209 ALL C T 7/25/320 0.071020 0.10470 9.118e-06
## 657760 10 rs2961608 ALL G C 26/73/246 0.211600 0.29670 4.607e-07
## 664027 10 rs11259036 ALL C T 4/9/319 0.027110 0.04989 6.506e-06
## 664096 10 rs17155248 ALL G A 21/62/247 0.187900 0.26550 8.710e-07
## 664786 10 rs11253609 ALL G A 5/15/331 0.042740 0.06869 8.472e-06
## 665821 10 rs2497828 ALL C T 70/123/154 0.354500 0.47070 3.513e-06
## 668584 10 rs7101296 ALL C T 37/89/214 0.261800 0.36450 7.265e-07
## 673000 10 rs211379 ALL G A 35/95/217 0.273800 0.36250 8.629e-06
## 676270 10 rs11238689 ALL C A 18/45/285 0.129300 0.20570 3.779e-09
## 682003 10 rs7070457 ALL G C 29/46/248 0.142400 0.27010 4.087e-14
## 686068 10 rs10995932 ALL C T 12/38/293 0.110800 0.16440 6.786e-07
## 687439 10 rs10762143 ALL G A 87/114/118 0.357400 0.49530 4.483e-07
## 708760 10 rs17130133 ALL C T 7/17/311 0.050750 0.08826 2.715e-07
## 710395 10 rs17094724 ALL G A 7/19/323 0.054440 0.09009 6.073e-07
## 712381 10 rs2420703 ALL T C 7/18/329 0.050850 0.08631 3.235e-07
## 712921 10 rs11199747 ALL G A 27/74/228 0.224900 0.31340 1.117e-06
## 718090 10 rs4751101 ALL A C 8/26/307 0.076250 0.11560 2.679e-06
## 719488 10 rs11017929 ALL C T 18/188/138 0.546500 0.43920 3.439e-06
## 731848 11 rs11026518 ALL A C 15/50/280 0.144900 0.20500 1.753e-06
## 733867 11 rs7123118 ALL T C 41/83/194 0.261000 0.38430 2.072e-08
## 733966 11 rs7107869 ALL C T 58/108/163 0.328300 0.44910 1.017e-06
## 735352 11 rs3858431 ALL C T 25/73/237 0.217900 0.29980 2.867e-06
## 739369 11 rs2061640 ALL C T 6/3/340 0.008596 0.04206 2.147e-11
## 744046 11 rs526821 ALL G A 78/127/148 0.359800 0.48030 2.230e-06
## 744184 11 rs17510445 ALL G T 12/27/305 0.078490 0.13730 2.510e-09
## 746338 11 rs7924942 ALL C T 19/46/279 0.133700 0.21440 2.125e-09
## 747955 11 rs314779 ALL G T 10/171/165 0.494200 0.39970 5.009e-06
## 749914 11 rs11236181 ALL C A 16/48/284 0.137900 0.20350 2.030e-07
## 756691 11 rs17193643 ALL C T 15/41/289 0.118800 0.18460 3.418e-08
## 757393 11 rs11019401 ALL G C 10/32/312 0.090400 0.13610 8.137e-07
## 774541 11 rs10893442 ALL T G 17/47/284 0.135100 0.20570 3.689e-08
## 775705 11 rs11221013 ALL A T 13/47/271 0.142000 0.19620 9.867e-06
## 779641 11 rs12574564 ALL G A 6/160/191 0.448200 0.36570 7.188e-06
## 783808 12 rs11056665 ALL C T 17/58/259 0.173700 0.23750 6.727e-06
## 786364 12 rs11055477 ALL G T 14/44/283 0.129000 0.18890 6.049e-07
## 788854 12 rs10450676 ALL G A 10/18/326 0.050850 0.10160 3.326e-10
## 792823 12 rs3825246 ALL G A 50/103/171 0.317900 0.43030 3.616e-06
## 793177 12 rs7294633 ALL C T 51/106/169 0.325200 0.43450 5.233e-06
## 796345 12 rs1607040 ALL C G 12/35/303 0.100000 0.15440 1.396e-07
## 802999 12 rs10783767 ALL G A 71/119/141 0.359500 0.47760 5.177e-06
## 810238 12 rs6582220 ALL G A 8/22/322 0.062500 0.10210 3.132e-07
## 812179 12 rs17046167 ALL C T 10/27/314 0.076920 0.12490 8.215e-08
## 813448 12 rs17009733 ALL G C 14/45/271 0.136400 0.19670 1.397e-06
## 820618 12 rs4764927 ALL G T 53/109/169 0.329300 0.43860 7.232e-06
## 824662 12 rs4964596 ALL T C 41/97/212 0.277100 0.38060 7.588e-07
## 825199 12 rs17760337 ALL C T 21/59/247 0.180400 0.26120 2.905e-07
## 825298 12 rs888551 ALL C T 21/65/239 0.200000 0.27500 3.754e-06
## 826558 12 rs7970839 ALL G A 11/31/289 0.093660 0.14730 1.901e-07
## 836122 12 rs4964998 ALL A C 11/41/305 0.114800 0.16090 6.186e-06
## 839842 13 rs3117848 ALL A G 15/40/277 0.120500 0.18860 3.595e-08
## 843229 13 rs623441 ALL A G 10/34/292 0.101200 0.14780 3.119e-06
## 846985 13 rs7986707 ALL C G 84/135/144 0.371900 0.48630 6.987e-06
## 847024 13 rs2875298 ALL C T 6/20/327 0.056660 0.08654 8.168e-06
## 854482 13 rs9538095 ALL C G 45/209/82 0.622000 0.49390 2.485e-06
## 857014 13 rs2324687 ALL C T 15/50/281 0.144500 0.20450 1.687e-06
## 858691 13 rs11618357 ALL A G 37/89/200 0.273000 0.37500 1.997e-06
## 858796 13 rs17086184 ALL C T 18/50/274 0.146200 0.21980 5.813e-08
## 861685 13 rs1954138 ALL C T 78/110/137 0.338500 0.48350 4.301e-08
## 871960 13 rs725834 ALL T G 27/201/123 0.572600 0.46260 8.029e-06
## 879550 13 rs12583597 ALL G A 8/18/310 0.053570 0.09607 4.912e-08
## 879586 14 rs4983173 ALL T G 1/154/178 0.462500 0.35870 9.093e-10
## 881833 14 rs17106805 ALL C A 12/38/288 0.112400 0.16660 7.996e-07
## 895669 14 rs12100548 ALL G A 11/35/299 0.101400 0.15160 7.804e-07
## 905833 14 rs17703828 ALL C T 24/72/238 0.215600 0.29470 4.908e-06
## 908032 14 rs11623367 ALL A G 9/31/308 0.089080 0.13090 3.303e-06
## 909877 14 rs4900208 ALL A G 29/199/108 0.592300 0.47240 2.576e-06
## 913615 14 rs6575760 ALL G A 11/34/289 0.101800 0.15360 7.019e-07
## 915706 15 rs8034683 ALL G A 29/79/235 0.230300 0.31960 1.498e-06
## 919927 15 rs16960205 ALL C T 6/16/334 0.044940 0.07556 1.127e-06
## 922057 15 rs4924361 ALL A T 20/56/265 0.164200 0.24190 9.936e-08
## 925597 15 rs2011064 ALL G C 54/105/184 0.306100 0.42820 2.268e-07
## 926482 15 rs8043320 ALL T C 4/9/326 0.026550 0.04889 5.987e-06
## 932803 15 rs1531441 ALL G A 24/76/247 0.219000 0.29350 7.467e-06
## 936832 15 rs7166639 ALL A G 13/45/281 0.132700 0.18750 3.513e-06
## 936976 15 rs10851919 ALL T A 33/205/83 0.638600 0.48790 2.311e-08
## 937567 15 rs4778588 ALL C T 53/112/172 0.332300 0.43770 8.990e-06
## 946066 15 rs1879612 ALL C T 76/124/139 0.365800 0.48270 8.146e-06
## 951991 16 rs1079350 ALL A G 80/116/130 0.355800 0.48820 7.253e-07
## 954955 16 rs4781448 ALL C G 30/80/227 0.237400 0.32910 1.003e-06
## 956842 16 rs11865082 ALL A G 53/215/73 0.630500 0.49830 1.222e-06
## 960367 16 rs4787447 ALL T C 10/36/297 0.105000 0.14990 5.740e-06
## 965473 16 rs12596776 ALL C G 13/37/297 0.106600 0.16510 8.501e-08
## 978217 16 rs16958749 ALL G C 14/44/270 0.134100 0.19540 9.945e-07
## 982561 17 rs4968070 ALL A G 41/214/86 0.627600 0.49130 2.615e-07
## 983431 17 rs923375 ALL C T 20/62/251 0.186200 0.25940 1.860e-06
## 986212 17 rs8078037 ALL G A 1/136/218 0.383100 0.31320 1.384e-06
## 986962 17 rs1714984 ALL A G 34/91/213 0.269200 0.35980 5.760e-06
## 1009222 18 rs2580149 ALL C T 55/107/158 0.334400 0.44820 4.765e-06
## 1009660 18 rs616031 ALL T C 4/6/334 0.017440 0.03987 7.108e-07
## 1015924 18 rs9947011 ALL T C 28/76/214 0.239000 0.32890 2.944e-06
## 1024435 18 rs11878064 ALL G A 42/97/200 0.286100 0.39140 1.124e-06
## 1031545 18 snp_a-2228215 ALL C T 6/9/324 0.026550 0.06003 1.596e-08
## 1032442 18 rs11878133 ALL G A 6/14/322 0.040940 0.07313 4.684e-07
## 1032925 18 rs9807306 ALL A T 0/116/226 0.339200 0.28170 6.852e-06
## 1035019 18 rs12956627 ALL C T 8/19/307 0.056890 0.09930 9.277e-08
## 1041556 18 rs732771 ALL A G 12/31/302 0.089860 0.14670 2.256e-08
## 1050112 19 rs1102152 ALL T C 13/47/290 0.134300 0.18680 5.169e-06
## 1052599 19 rs10422017 ALL C T 65/110/155 0.333300 0.46280 3.480e-07
## 1052827 19 rs7412 ALL T C 13/29/322 0.079670 0.13970 6.600e-10
## 1053259 19 rs2974215 ALL C T 12/45/292 0.128900 0.17820 8.986e-06
## 1055227 19 rs10853870 ALL A G 24/203/121 0.583300 0.46120 6.504e-07
## 1064155 20 rs16993822 ALL C T 54/98/170 0.304300 0.43510 7.397e-08
## 1066621 20 rs6044761 ALL T G 12/41/298 0.116800 0.16800 1.834e-06
## 1069909 20 rs16985266 ALL G A 8/21/313 0.061400 0.10230 2.329e-07
## 1071013 20 rs8183079 ALL A G 63/120/173 0.337100 0.45230 1.728e-06
## 1073299 20 rs2179318 ALL C T 59/112/163 0.335300 0.45150 2.592e-06
## 1073302 20 rs7270784 ALL T C 51/113/196 0.313900 0.41890 3.499e-06
## 1082767 20 rs4810120 ALL T C 95/121/114 0.366700 0.49830 1.418e-06
## 1085788 21 rs2246835 ALL A G 10/178/149 0.528200 0.41490 1.365e-07
## 1091239 21 snp_a-2017079 ALL G A 28/76/230 0.227500 0.31710 8.070e-07
## 1099498 21 rs2838011 ALL G A 9/33/306 0.094830 0.13580 7.371e-06
## 1108249 22 rs743742 ALL A C 21/65/249 0.194000 0.26840 2.196e-06
## 1115374 22 rs2024700 ALL T G 31/87/223 0.255100 0.34150 7.743e-06
## 1123111 23 rs5928121 ALL C T 28/43/93 0.262200 0.42150 1.359e-06
## 1123741 23 rs6629045 ALL G A 8/15/133 0.096150 0.17900 3.136e-06
## 1130374 23 rs12398458 ALL G A 7/7/154 0.041670 0.11720 1.793e-08
## 1137220 23 rs2206232 ALL G A 11/21/121 0.137300 0.24160 2.553e-06
## P_bin minus_log10P
## 5539 1 5.273028
## 10975 1 6.050366
## 15025 1 5.514137
## 19678 1 7.495937
## 21265 1 5.386581
## 23785 1 6.655804
## 27025 1 6.540155
## 28645 1 5.573326
## 29527 1 5.480303
## 29614 1 7.974285
## 31561 1 5.084970
## 46723 1 5.601539
## 46822 1 6.167874
## 49084 1 8.002090
## 49750 1 5.023788
## 56656 1 5.070785
## 59926 1 5.083704
## 65890 1 5.772113
## 66598 1 5.211761
## 66700 1 5.724228
## 70558 1 5.325139
## 73417 1 5.855115
## 81343 1 5.612966
## 81937 1 5.023467
## 82291 1 6.447575
## 83707 1 5.988853
## 87778 1 6.873869
## 95533 1 5.053646
## 111655 1 5.011263
## 111925 1 5.787812
## 112390 1 5.427593
## 117274 1 6.503624
## 119263 1 5.258612
## 124063 1 5.638650
## 131515 1 5.326150
## 136447 1 5.119987
## 142570 1 5.514847
## 149569 1 6.318759
## 155782 1 12.378720
## 157828 1 5.053646
## 160444 1 7.181444
## 160534 1 5.214670
## 160978 1 5.610125
## 186715 1 5.443456
## 186979 1 6.028492
## 187279 1 8.994391
## 192580 1 7.691222
## 196513 1 6.403513
## 196750 1 5.125170
## 196813 1 5.777544
## 197365 1 5.257668
## 198562 1 5.330033
## 201574 1 5.128427
## 205732 1 5.005903
## 212689 1 5.077742
## 212713 1 5.138107
## 217693 1 5.824778
## 219823 1 5.730721
## 224422 1 5.290476
## 239239 1 5.113735
## 241954 1 5.051881
## 248263 1 5.095068
## 248719 1 5.823041
## 250339 1 5.988007
## 253483 1 5.074224
## 254362 1 5.542724
## 258370 1 7.369470
## 263617 1 5.373968
## 266386 1 9.253210
## 268561 1 6.369979
## 271756 1 5.092374
## 281524 1 5.086451
## 283720 1 5.197705
## 283780 1 6.200453
## 293845 1 5.066057
## 294445 1 5.823619
## 294652 1 7.231954
## 298777 1 6.835647
## 303172 1 7.000261
## 304864 1 5.436875
## 306601 1 5.668573
## 312376 1 5.209856
## 315193 1 5.564793
## 315691 1 5.396639
## 317419 1 5.007579
## 319504 1 6.148253
## 329668 1 5.127203
## 339097 1 6.112214
## 339139 1 5.324955
## 343795 1 5.546835
## 354736 1 6.164880
## 355492 1 5.905878
## 357592 1 6.287687
## 359584 1 7.322302
## 359716 1 6.926282
## 364009 1 7.569764
## 367591 1 9.374996
## 368005 1 6.094474
## 377116 1 5.044072
## 378994 1 6.037252
## 380134 1 8.253055
## 384943 1 5.732359
## 403423 1 8.071655
## 405823 1 5.484921
## 417547 1 5.293965
## 418000 1 8.000043
## 421120 1 5.073452
## 421801 1 7.090390
## 423724 1 5.293624
## 424291 1 5.591760
## 437122 1 5.744004
## 437350 1 6.671417
## 440485 1 5.235002
## 442045 1 6.093126
## 446575 1 5.397506
## 452491 1 6.515131
## 454087 1 7.524910
## 458545 1 5.186086
## 459394 1 7.257432
## 459424 1 5.273273
## 461680 1 5.177897
## 463009 1 5.288193
## 470494 1 7.357041
## 470719 1 6.185153
## 475855 1 5.311936
## 481057 1 6.382057
## 482059 1 5.679023
## 488632 1 5.962175
## 503485 1 8.722849
## 504871 1 5.110026
## 507385 1 6.792904
## 508285 1 7.439137
## 512086 1 5.764724
## 519808 1 5.696588
## 522961 1 6.253521
## 525394 1 5.187889
## 525580 1 5.056258
## 526900 1 5.319937
## 528502 1 8.594312
## 529885 1 7.709743
## 530143 1 8.904134
## 534766 1 5.133890
## 536764 1 5.825649
## 539056 1 5.849858
## 539815 1 7.234331
## 548686 1 5.142969
## 552811 1 5.564315
## 556678 1 6.620876
## 568729 1 6.081079
## 574618 1 5.057446
## 575473 1 5.981300
## 578194 1 5.008552
## 579004 1 9.942714
## 585775 1 5.165961
## 595174 1 6.433680
## 599152 1 7.011932
## 602005 1 7.526513
## 602695 1 5.014035
## 605794 1 5.100508
## 608512 1 5.064493
## 613915 1 7.374688
## 614257 1 6.530915
## 620695 1 5.176200
## 634354 1 5.232251
## 639478 1 7.679854
## 649807 1 5.707522
## 650857 1 5.001523
## 655102 1 5.040100
## 657760 1 6.336582
## 664027 1 5.186686
## 664096 1 6.059982
## 664786 1 5.072014
## 665821 1 5.454322
## 668584 1 6.138764
## 673000 1 5.064040
## 676270 1 8.422623
## 682003 1 13.388595
## 686068 1 6.168386
## 687439 1 6.348431
## 708760 1 6.566230
## 710395 1 6.216597
## 712381 1 6.490126
## 712921 1 5.951947
## 718090 1 5.572027
## 719488 1 5.463568
## 731848 1 5.756218
## 733867 1 7.683610
## 733966 1 5.992679
## 735352 1 5.542572
## 739369 1 10.668168
## 744046 1 5.651695
## 744184 1 8.600326
## 746338 1 8.672641
## 747955 1 5.300249
## 749914 1 6.692504
## 756691 1 7.466228
## 757393 1 6.089536
## 774541 1 7.433091
## 775705 1 5.005815
## 779641 1 5.143392
## 783808 1 5.172179
## 786364 1 6.218316
## 788854 1 9.478078
## 792823 1 5.441772
## 793177 1 5.281249
## 796345 1 6.855115
## 802999 1 5.285922
## 810238 1 6.504178
## 812179 1 7.085392
## 813448 1 5.854804
## 820618 1 5.140742
## 824662 1 6.119873
## 825199 1 6.536854
## 825298 1 5.425506
## 826558 1 6.721018
## 836122 1 5.208590
## 839842 1 7.444301
## 843229 1 5.505985
## 846985 1 5.155709
## 847024 1 5.087884
## 854482 1 5.604674
## 857014 1 5.772885
## 858691 1 5.699622
## 858796 1 7.235600
## 861685 1 7.366431
## 871960 1 5.095339
## 879550 1 7.308742
## 879586 1 9.041293
## 881833 1 6.097127
## 895669 1 6.107683
## 905833 1 5.309095
## 908032 1 5.481091
## 909877 1 5.589054
## 913615 1 6.153725
## 915706 1 5.824488
## 919927 1 5.948076
## 922057 1 7.002788
## 925597 1 6.644357
## 926482 1 5.222791
## 932803 1 5.126854
## 936832 1 5.454322
## 936976 1 7.636200
## 937567 1 5.046240
## 946066 1 5.089056
## 951991 1 6.139482
## 954955 1 5.998699
## 956842 1 5.912929
## 960367 1 5.241088
## 965473 1 7.070530
## 978217 1 6.002395
## 982561 1 6.582528
## 983431 1 5.730487
## 986212 1 5.858864
## 986962 1 5.239578
## 1009222 1 5.321937
## 1009660 1 6.148253
## 1015924 1 5.531062
## 1024435 1 5.949234
## 1031545 1 7.796967
## 1032442 1 6.329383
## 1032925 1 5.164183
## 1035019 1 7.032592
## 1041556 1 7.646661
## 1050112 1 5.286593
## 1052599 1 6.458421
## 1052827 1 9.180456
## 1053259 1 5.046434
## 1055227 1 6.186819
## 1064155 1 7.130944
## 1066621 1 5.736601
## 1069909 1 6.632831
## 1071013 1 5.762456
## 1073299 1 5.586365
## 1073302 1 5.456056
## 1082767 1 5.848324
## 1085788 1 6.864867
## 1091239 1 6.093126
## 1099498 1 5.132474
## 1108249 1 5.658368
## 1115374 1 5.111091
## 1123111 1 5.866781
## 1123741 1 5.503624
## 1130374 1 7.746420
## 1137220 1 5.592949
##
## $p_hwe
##MAF fails
fail_maf <- check_maf(indir, name, qcdir=indir, path2plink=path2plink,
mafTh=0.01, macTh=NULL,
interactive=TRUE, verbose=TRUE, showPlinkOutput=FALSE)## File with individuals that failed perIndividualQC: C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas.fail.IDs does not exist. Continue check_maf for all samples in C:/Users/GrandProf/Documents/adgwas1/plink_win64_20220402/input/binary_adgwas.fam## The mafTh is 0.01 which corresponds to a mcfTh=7.28
SNP QC
fail_markers <- perMarkerQC(indir=indir, qcdir=qcdir, name=name, path2plink=path2plink,
lmissTh = 0.10,
hweTh = 1e-05,
mafTh=0.01, macTh=NULL,
verbose=TRUE, interactive=TRUE, showPlinkOutput=FALSE)## Identification of SNPs with high missingness rate## Identification of SNPs with deviation from HWE## Remove markers with a low minor allele frequency## The mafTh is 0.01 which corresponds to a mcfTh=7.08
overview_marker <- overviewPerMarkerQC(fail_markers, interactive=TRUE)
Create a clean data set
Ids <- cleanData(indir=indir, qcdir=qcdir, name=name, path2plink=path2plink,
filterSex=FALSE, filterRelated=FALSE, filterAncestry=FALSE,
verbose=TRUE, showPlinkOutput=FALSE)## Read individual IDs that failed heterozygosity check## Read individual IDs that failed missingness check## No individuals failed missingness check## Write file with remove IDs## The macTh is 20 which corresponds to a mafTh=0.028249## Remove individual IDs and markers IDs that failed QCRun the association test
assoc = paste(path2plink, ' --bfile ', qcdir, '/', name, '.clean --logistic --allow-no-sex --ci 0.95 --out ', qcdir, '/load', sep='')
system(assoc, intern=FALSE)## [1] 0No HapMap corrections
- Not that i know what that means but we fail to perform hapmap corrections
- check out detailed code for that
- this is just a technical skill check to ensure that i know what is going on in R
- i have a rough idea what is happening but like 5%
Application to lupus
- The hope is to apply this in improving gwas studies on lupus