library(bigsnpr)
bed <- "../Dubois2010_data/FinnuncorrNLITUK3hap550.bed"
system.time(
test <- snp_readBed(bed, tempfile())
)
# 54 / 78
G <- snp_attach(test)$genotypes
system.time(big_counts(G))
system.time(big_counts(G))
system.time(big_counts(G))
n <- fpeek::peek_count_lines(sub("\\.bed$", ".fam", bed))
p <- fpeek::peek_count_lines(sub("\\.bed$", ".bim", bed))
c(n, p)
system.time(FBM.code256(n, p, code = bigsnpr:::CODE_012, init = 2L))
# 35 sec
system.time({
X <- FBM.code256(n, p, code = bigsnpr:::CODE_012)
system.time(
read_plink(X, bed, n, p, decode = bigsnpr:::getCode())
)
})
# 41 / 54
# system.time({
# X <- FBM.code256(n, p, code = bigsnpr:::CODE_012)
# big_parallelize(X, p.FUN = function(X, ind, read, bed, n, p) {
# read(X, bed, n, p, decode = bigsnpr:::getCode(), ind_col = ind)
# }, p.combine = unlist, ind = seq_len(p), ncores = 2,
# read = bigsnpr:::read_plink, bed = bed, n = n, p = p)
# })
# 49 / 65
# parallelism is useless, as always when writing to disk
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