read.stack.R: reads a list of files into a single data.frame and allows you to add extra columns to each

read.stack.R

read.stack <- function(files, ..., select=NULL, extra=NULL, reader=read.table) {
    dd<-data.frame()
    if(!is.null(extra)) {
        stopifnot(is.list(extra))
        stopifnot(all(sapply(extra, length)==length(files)))
    }
    for(i in 1:length(files)) {
        d<-reader(files[i], ...)
        if(!is.null(select)) {
            stopifnot(all(select %in% names(d)))
            d<-d[, select]
        }
        if(!is.null(extra)) {
            d<-do.call(cbind, c(list(d), lapply(extra, '[', i)))
        }
        if(nrow(dd)>0) {
            dd<-rbind(dd, d)
        } else {
            dd<-d
        }
    }
    dd
}

test.read.stack.R

#paste0 <- function(...) paste(..., sep="")

regions <- c("exome","chr20")
conditions <- c("exp1","exp2","exp3")

opts <- expand.grid(cond=conditions, region=regions)

dd <- read.stack(paste0("comp.", opts$region, "/", opts$cond, ".txt"), header=T, extra=opts)