Read a blacklist object or file.
Used internally in radiator and might be of interest for users.
read_blacklist_genotypes(blacklist.genotypes = NULL, verbose = FALSE, ...)(path or object)
The blacklist is an object in your
global environment or a file in the working directory (e.g. "blacklist.geno.tsv").
The dataframe contains at least these 2 columns: MARKERS, INDIVIDUALS.
Additional columns are allowed: CHROM, LOCUS, POS.
Useful to erase genotypes with bad QC, e.g. genotype with more than 2 alleles in diploid likely sequencing errors or genotypes with poor genotype likelihood or coverage.
Columns are cleaned of separators that interfere with some packages or codes, detailed in
clean_markers_names and clean_ind_names
Default blacklist.genotypes = NULL.
(optional, logical) When verbose = TRUE
the function is a little more chatty during execution.
Default: verbose = TRUE.
(optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)
This function arguments will be subject to changes. Currently the function uses
erase.genotypes, but using the dots-dots-dots ... arguments allows to
pass erase.genotypes and masked.genotypes. These arguments do exactly
the same thing and only one can be used.
if (FALSE) { # \dontrun{
bl <- radiator::read_blacklist_genotypes(data = data,
blacklist.genotypes = "blacklist.geno.iguana.tsv")
} # }