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read blacklist of genotypes

Source: R/filter_blacklist_genotypes.R
read_blacklist_genotypes.Rd

Read a blacklist object or file.

Used internally in radr and might be of interest for users.

Usage

read_blacklist_genotypes(blacklist.genotypes = NULL, verbose = FALSE, ...)

Arguments

blacklist.genotypes

(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.

verbose

Logical indicating whether progress messages are emitted. Default: verbose = TRUE.

...

Additional arguments passed to lower-level screening or filtering functions.

Life cycle

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.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
bl <- radr::read_blacklist_genotypes(data = data,
    blacklist.genotypes = "blacklist.geno.iguana.tsv")
} # }