Read and write GRM from GCTA

grm_io.R

readGRM <- function(rootname)
{
	bin.file.name <- paste(rootname, ".grm.bin", sep="")
	n.file.name <- paste(rootname, ".grm.N.bin", sep="")
	id.file.name <- paste(rootname, ".grm.id", sep="")

	cat("Reading IDs\n")
	id <- read.table(id.file.name, colClasses="character")
	n <- dim(id)[1]
	cat("Reading GRM\n")
	bin.file <- file(bin.file.name, "rb")
	grm <- readBin(bin.file, n=n*(n+1)/2, what=numeric(0), size=4)
	close(bin.file)
	cat("Reading N\n")
	n.file <- file(n.file.name, "rb")
	N <- readBin(n.file, n=n*(n+1)/2, what=numeric(0), size=4)
	close(n.file)

	cat("Creating data frame\n")
	l <- list()
	for(i in 1:n)
	{
		l[[i]] <- 1:i
	}
	col1 <- rep(1:n, 1:n)
	col2 <- unlist(l)
	grm <- data.frame(id1=col1, id2=col2, N=N, grm=grm)	

	ret <- list()
	ret$grm <- grm
	ret$id <- id
	return(ret)
}

writeGRM <- function(grm, rootname)
{
	bin.file.name <- paste(rootname, ".grm.bin", sep="")
	n.file.name <- paste(rootname, ".grm.N.bin", sep="")
	id.file.name <- paste(rootname, ".grm.id", sep="")
	write.table(grm$id[,1:2], id.file.name, row=F, col=F, qu=F)
	n <- dim(id)[1]
	cat("Writing GRM\n")
	bin.file <- file(bin.file.name, "wb")
	writeBin(grm$grm$grm, bin.file, size=4)
	close(bin.file)
	cat("Writing N\n")
	n.file <- file(n.file.name, "wb")
	writeBin(grm$grm$N, n.file, size=4)
	close(n.file)
}

grm <- readGRM("filename")
writeGRM(grm, "filename2")