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# grab annotation information for the MUGA arrays
# subset and place in data/
library(here)
library(data.table)
url <- "https://raw.githubusercontent.com/kbroman/MUGAarrays/main/UWisc/"
files <- c(gm="gm_uwisc_v4.csv",
mm="mm_uwisc_v4.csv",
mini="mini_uwisc_v5.csv",
muga="muga_uwisc_v4.csv")
MUGAmaps <- as.list(files)
col2keep <- c("marker", "chr", "bp_grcm39", "cM_cox")
for(i in seq_along(files)) {
file <- files[i]
local_file <- here("inst/scripts", file)
# download file
if(!file.exists(local_file)) {
download.file(paste0(url, file), local_file)
}
# read file
tmp <- data.table::fread(local_file, data.table=FALSE)
# subset to unique, mapped, on chr 1-19, X
tmp <- tmp[tmp$unique & !tmp$unmapped & !is.na(tmp$chr) &
tmp$chr %in% c(1:19,"X") & !is.na(tmp$bp_grcm39), col2keep]
tmp <- tmp[order(factor(tmp$chr, c(1:19,"X")), tmp$bp_grcm39),]
MUGAmaps[[i]] <- tmp
}
save(MUGAmaps, file=here("data", "MUGAmaps.RData"), compress=TRUE)
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