`setupSNP` <-
function(data, colSNPs, sort=FALSE, info, sep="/", ...)
{
if (missing(data))
stop("Required argument data is missing")
if (is.matrix(data))
data<-as.data.frame(data)
if (!is.data.frame(data))
stop("Argument data is not a data.frame or matrix")
if (sort)
{
temp <- sortSNPs(data, colSNPs, info)
pos <- temp$pos
info <- temp$dataSorted
temp <- data[, pos, drop=FALSE]
#..debug..# dataSNPs <- mclapply(temp, snp, sep = sep, ...)
dataSNPs <- lapply(temp, snp, sep = sep, ...)
}
else
{
#..debug..# dataSNPs <- mclapply(data[, colSNPs, drop=FALSE], snp, sep = sep, ...)
dataSNPs <- lapply(data[, colSNPs, drop=FALSE], snp, sep = sep, ...)
}
dataSNPs <- data.frame(dataSNPs)
datPhen <- data[ , -colSNPs, drop=FALSE]
ans<-cbind(datPhen,dataSNPs)
label.SNPs <- names(dataSNPs)
class(ans) <- c("setupSNP","data.frame")
attr(ans,"row.names") <- 1:length(ans[[1]])
attr(ans,"label.SNPs") <- label.SNPs
attr(ans,"colSNPs") <- c( (length(ans) - length(label.SNPs)+1) : length(ans))
if (sort)
attr(ans,"gen.info") <- info
ans
}
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