# read cross input from qtl package
readlgcross <- function(cross, mapthese)
{
if (!requireNamespace("qtl", quietly = TRUE)) {
stop("Please install package qtl")
}
# if list not provided create list of all using chrnames function of qtl
if (missing(mapthese)) {
mapthese <- qtl::chrnames(cross)
}
else {
if (!all(mapthese %in% qtl::chrnames(cross))) {
stop ("chrnames to map not found in cross object")
}
}
df <- qtl::pull.map(cross, mapthese, as.table = TRUE)
# remove factors if any
fas <- sapply(df, is.factor)
df[fas] <- lapply(df[fas], as.character)
df$locus <- rownames(df)
# assign my own column names so I can reference by name
colnames(df) <- c("group", "position", "locus")
return (df)
}
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