source('R/utils.R')
BedToBig4 <- function(bedfile,
block.size,
backingfile,
backingpath = "backingfiles") {
checkExists(backingfile, backingpath)
# check extension of file
ext <- tools::file_ext(bedfile)
if (ext != "bed") {
stop(sprintf("Extension .%s unsupported, requires .bed instead", ext))
} else {
bimfile <- sub("\\.bed$", ".bim", bedfile)
famfile <- sub("\\.bed$", ".fam", bedfile)
}
# check if all three files exist
if (!file.exists(bedfile)) {
stop(sprintf("File \"%s\" doesn't exist", bedfile))
} else if (!file.exists(bimfile)) {
stop(sprintf("File \"%s\" doesn't exist", bimfile))
} else if (!file.exists(famfile)) {
stop(sprintf("File \"%s\" doesn't exist", famfile))
}
# read map and family files
fam <- data.table::fread(famfile, data.table = FALSE)
names(fam) <- c("family.ID", "sample.ID", "paternal.ID",
"maternal.ID", "sex", "affection")
bim <- data.table::fread(bimfile, data.table = FALSE)
names(bim) <- c("chromosome", "marker.ID", "genetic.dist",
"physical.pos", "allele1", "allele2")
# prepare big.matrix
n <- nrow(fam)
m <- nrow(bim)
bsz <- ceiling(n/4)
bigGeno <- bigmemory::big.matrix(bsz, m, type = "raw",
backingfile = paste0(backingfile, ".bk"),
backingpath = backingpath,
descriptorfile = paste0(backingfile, ".desc"))
## open bed file and check its magic number
bed <- file(bedfile, open = "rb")
magic <- readBin(bed, "raw", 3)
if (!all(magic == c("6c", "1b", "01"))) {
stop("Wrong magic number for bed file; should be -- 0x6c 0x1b 0x01 --.")
}
# now actually read genotypes block by block
intervals <- CutBySize(m, block.size)
nb.blocks <- nrow(intervals)
if (intr <- interactive())
pb <- utils::txtProgressBar(min = 0, max = nb.blocks, style = 3)
colOffset <- 0L
for (k in 1:nb.blocks) {
size <- intervals[k, "size"]
bigGeno[, 1:size + colOffset] <-
readBin(bed, what = "raw", n = bsz * size)
colOffset <- colOffset + size
if (intr) utils::setTxtProgressBar(pb, k)
}
close(bed)
if (intr) close(pb)
snp_list <- list(genotypes = bigGeno, fam = fam, map = bim,
backingfile = backingfile,
backingpath = backingpath)
class(snp_list) <- "bigSNP"
saveRDS(snp_list, file.path(backingpath, paste0(backingfile, ".rds")))
snp_list
}
bedfile2 <- "../Dubois2010_data/FinnuncorrNLITUK1UK3hap300.bed"
print(system.time(
celiacRaw <- BedToBig4(bedfile2, block.size = 500, backingfile = "celiacRaw")
))
# 74 sec just to read binary to logical
# 89 sec write raw data
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