knitr::opts_chunk$set(echo = TRUE)
Convert from save
/load
to saveRDS
/readRDS
. Should improve access but will not change size.
suppressPackageStartupMessages({ library(qtl2geno) library(DOread) library(qtl2feather) }) dirpath <- file.path("~/Documents/Research/attie_alan/DO", "data") datapath <- file.path(dirpath, "DerivedData")
Set up feather directory.
pmap <- readRDS(file.path(datapath, "pmap.rds")) feather_dir <- file.path(datapath, "feather") if(!dir.exists(feather_dir)) dir.create(feather_dir)
Genotype allele probabilities (slow)
aprobs <- DOread::read_probs(NULL, datapath = datapath, method = "calc")$probs faprobs <- qtl2feather::feather_genoprob(aprobs, "aprobs", feather_dir, verbose = FALSE) saveRDS(faprobs, file = file.path(feather_dir, "faprobs.rds"))
Genotype 36 probabilities (very slow).
chr <- names(pmap)[1] probs <- DOread::read_probs(chr, datapath = datapath, allele = FALSE, method = "calc")$probs fprobs <- qtl2feather::feather_genoprob(probs, "probs", feather_dir, verbose = FALSE) for(chr in names(pmap)[-1]) { cat(chr, "\n") probs <- DOread::read_probs(chr, datapath = datapath, allele = FALSE, method = "calc")$probs fprobs <- cbind(fprobs, qtl2feather::feather_genoprob(probs, "probs", feather_dir, verbose = FALSE)) } saveRDS(fprobs, file = file.path(feather_dir, "fprobs.rds"))
system(paste("ls -lh", feather_dir))
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