View source: R/filter_blacklist_genotypes.R
read_blacklist_genotypes | R Documentation |
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, ...)
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: 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
|
verbose |
(optional, logical) When |
... |
(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.
Thierry Gosselin thierrygosselin@icloud.com
## Not run:
bl <- radiator::read_blacklist_genotypes(data = data,
blacklist.genotypes = "blacklist.geno.iguana.tsv")
## End(Not run)
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