#' Date: 2016-11-21
#' Object: Optimize pruning step
#' Results:
require(bigsnpr)
celiac2 <- AttachBigSNP("celiac_sub2_impute1",
"../thesis-celiac/backingfiles/")
print(dim(celiac2$genotypes))
# print(system.time(BigToBed(celiac2, "tmp-files/celiac-imputed.bed")))
# 50 sec
print(system.time(
test <- PrunePlink(celiac2, size = 50, thr.corr = 0.5, ncores = 6)
)) # 38 sec versus 2h30
# after plink --indep-pairwise 50 5 0.5
snps <- scan("../plink-1.07-x86_64/test-celiac.prune.in", what = "character")
ind2 <- which(celiac2$map$marker.ID %in% snps)
print(mean(ind2 %in% test)) # 99.6%
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