In byandell/DOread: Read DO data

knitr::opts_chunk$set(echo = TRUE)

R Markdown

Convert from save/load to saveRDS/readRDS. Should improve access but will not change size.

library(readr)
library(qtl2geno)
dirpath <- file.path("~/Documents/Research/attie_alan/DO", "data")
datapath <- file.path(dirpath, "DerivedData/wave4")

Precomputed peaks

load(file.path(datapath, "peaks.RData"))
saveRDS(peaks, file.path(datapath, "peaks.rds"))

Precomputed analyses

analysis_tbl <- read_csv(file.path(datapath, "analyses.csv"))
saveRDS(analysis_tbl, file.path(datapath, "analyses.rds"))

Genotype probabilities (slow)

## Genotype probabilities ("probs") [very large]
load(file.path(datapath, 
               "GM_Attie_allele_call_haploprobs_4qtl2_wave4.Rdata"))
load(file.path(datapath, "markers.RData"))
for(i in seq(along=probs$map)) {
  tmp <- names(probs$map[[i]])
  probs$map[[i]][tmp] <- markers[tmp, 3]
}

## physical map of the markers in the probs array
load(file.path(datapath, "pmap.RData"))
saveRDS(pmap, file.path(datapath, "pmap.rds"))
saveRDS(probs, file.path(datapath, "probs.rds"))
for(chr in names(probs$map)) {
  cat(chr, "\n")
  saveRDS(probs[,chr], 
          file.path(datapath, paste0("probs_", chr, ".rds")))
}

Kinship matrices ("loco" method) ("K")

load(file.path(datapath, "kinship.RData"))
saveRDS(K, file.path(datapath, "kinship.rds"))

Covariates

load(file.path(datapath, "covar.RData"))
saveRDS(covar, file.path(datapath, "covar.rds"))

Phenotypes

for(pheno_type in c("clin","otu","otufam")) {
  tmp <- paste("pheno", pheno_type, sep = "_")
  tmp2 <- paste(tmp, "dict", sep = "_")
  load(file.path(datapath, paste0(tmp, ".RData")))
  saveRDS(get(tmp), file.path(datapath, paste0(tmp, ".rds")))
  saveRDS(get(tmp2), file.path(datapath, paste0(tmp2, ".rds")))
}

Put in new OTU measurements.

analysis_tbl <- read_csv(file.path(datapath, "wave4", "DOQTL",
                                   "analyses.csv"))
saveRDS(analysis_tbl, file.path(datapath, "analyses.rds"))
load(file.path(datapath, "wave4", "DOQTL", "peaks.Rdata"))
load(file.path(datapath, "wave4", "DOQTL", "pheno_otu.Rdata"))
saveRDS(peaks, file.path(datapath, "peaks.rds"))
saveRDS(pheno_otu, file.path(datapath, "pheno_otu.rds"))
saveRDS(pheno_otu_dict, file.path(datapath, "pheno_otu_dict.rds"))