Help with a function [along columns]
On Mon, 13 Oct 2014 08:54:51 PM Kate Ignatius wrote:
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.
Hi Kate, Unless you have passed "vcf" to your function, it is unlikely to recognize it. As you are working with genome data, I suspect that there is a function named "vcf" somewhere in the parent environment and you can't subset a function. Jim