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## Functions that are in early development for eQTL analysis project ##
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## Author: Dan Evans
## Last update: 2016-10-13
#function to mark SNPs where the coded alleles from the study data must be switched to match the effect alleles reported from previous GWAS
alleleCheck <- function(mydat){
#GWAS alleles are effect_allele and non_effect_allele
#Cohort alleles are coded_all and noncoded_all
mydat[ ,effect_allele:=toupper(effect_allele ) ]
mydat[ ,non_effect_allele:=toupper(non_effect_allele) ]
mydat[ ,coded_all:=toupper(coded_all) ]
mydat[ ,noncoded_all:=toupper(noncoded_all) ]
#test for same alleles
mydat[,noMatch:=0]
mydat[effect_allele!=coded_all | non_effect_allele!=noncoded_all , noMatch:=1]
#test if switching coding and non-coding alleles solves non-matching.
mydat[ , allele_switch:=0]
mydat[noMatch==1 & effect_allele==noncoded_all & non_effect_allele==coded_all, allele_switch:=1 ]
return(mydat[noMatch==1 & allele_switch==0, .N ])
}
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