|
#' Read binary GRM files into R |
|
#' |
|
#' @param rootname |
|
#' @export |
|
#' @return List of GRM and id data frames |
|
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) |
|
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) |
|
} |
|
|
|
#' Write readGRM style output back to binary GRM for use with GCTA |
|
#' |
|
#' @param grm Output from \link{readGRM} |
|
#' @param rootname |
|
#' @export |
|
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$id, id.file.name, row=F, col=F, qu=F) |
|
n <- dim(grm$id)[1] |
|
bin.file <- file(bin.file.name, "wb") |
|
writeBin(grm$grm$grm, bin.file, size=4) |
|
close(bin.file) |
|
n.file <- file(n.file.name, "wb") |
|
writeBin(grm$grm$N, n.file, size=4) |
|
close(n.file) |
|
} |
|
|
|
|
|
setUnrelsZero <- function(grm, threshold) |
|
{ |
|
index <- grm$grm$grm < threshold |
|
grm$grm$grm[index] <- 0 |
|
return(grm) |
|
} |
|
|
|
|
|
arguments <- commandArgs(T) |
|
|
|
infile <- arguments[1] |
|
outfile <- arguments[2] |
|
threshold <- as.numeric(arguments[3]) |
|
|
|
grm <- readGRM(infile) |
|
grm <- setUnrelsZero(grm, threshold) |
|
writeGRM(grm, outfile) |
