Created
April 19, 2017 20:55
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Descriptive statistics for genotype merge discordances
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#Merge data in PLINK, using merge mode 6 or 7 | |
./plink --bfile YEHUDA --bmerge YEHUDA.bed YEHUDA.bim YEHUDA.fam --merge-mode 7 --out yehude-merge | |
R | |
setwd('F:/rutgers_2') | |
dat <- read.table('yehude-merge.diff', header=T,nr=800000,stringsAsFactors=F) | |
library(plyr) | |
#Determine general amount of disagreement for each SNP. Ones that have especially high disagreement may be badly genotyped | |
quantile(table(dat$SNP)) | |
#Plot it | |
hist(table(dat$SNP) ) | |
#Count discordances for each subject by getting dimension of data | |
#Returns a dataframe with N merged subjects rows, column 2 is the number of discordances | |
dimcheck <- ddply(dat, ~IID, dim) | |
#See average discordances by subject |
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