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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.