Hi all,
I need help with a function. I'm trying to write a function to apply
to varying number of columns in a lot of files - hence the function...
but I'm getting stuck. Here it is:
gt<- function(x) {
alleles <- sapply(x, function(.) strsplit(as.character(.), "/"))
gt <- apply(x, function(.) ifelse(x[1] == vcf[3] & x[2] == vcf[3], 'RR',
ifelse(x[1] == vcf[4] & x[2] == vcf[4], 'AA',
ifelse(x[1] == vcf[3] & x[2] == vcf[4], 'RA',
ifelse(x[1] == vcf[4] & x[2] == vcf[3], 'RA', '')))))
}
I have different sized family genetic files and at the end of the day
I want to see whether the alleles of each person in the family match
the ref and/or the alt and if so, give AA, RA or RR.
Like so:
REF ALT Sample_1 GT_1 Sample_2 GT_2
A G A/A RR A/G RA
T G G/G AA T/T RR
A T T/T AA A/A RR
G A G/A RA G/G RR
G A G/G RR G/A RA
T C C/C AA C/C AA
T C C/C AA C/C AA
C T C/T RA T/T AA
G A A/A AA A/A AA
T G T/G RA G/G AA
Is there an easy way to do this?
Thanks!
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