R help - Oct 2014 - Help with a function [along columns]

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!

Just an update to this:

gtal <- function(d) {
    alleles <- sapply(d, function(.) strsplit(as.character(.),
"/"))
    gt <- unlist(lapply(alleles, function(x)
           ifelse(identical(x[[1]], vcf[,3]) & identical(x[[2]], vcf[,3]),
'RR',
           ifelse(identical(x[[1]], vcf[,4]) & identical(x[[2]], vcf[,4]),
'AA',
           ifelse(identical(x[[1]], vcf[,3]) & identical(x[[2]], vcf[,4]),
'RA',
           ifelse(identical(x[[1]], vcf[,4]) & identical(x[[2]],
vcf[,3]), 'RA', ''))))))
}

I've got something working but I'm having trouble with the gt part...
I'm getting the error: object of type 'closure' is not subsettable.
The vcf is my original file that I want to match with so not sure
whether this a problem.

On Mon, Oct 13, 2014 at 4:46 PM, Kate Ignatius <kate.ignatius at
gmail.com> wrote:
> 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!