Given a "vcfLink" object, removes loci/samples corresponding to a set of filtering options.
1 2 3 4 5 6 7 8 9 10 | Filter(object, ...)
## S4 method for signature 'vcfLink'
Filter(object, arguments = filterOptions(),
indels = c("keep", "remove", "only"), verbose = TRUE)
filterOptions(min.meanDP = NULL, max.meanDP = NULL, minDP = NULL,
maxDP = NULL, min.alleles = NULL, max.alleles = NULL, maf = NULL,
max.maf = NULL, minQ = NULL, max.missing = NULL, hwe = NULL,
thin = NULL)
|
object |
an object of class "vcfLink" |
arguments |
optional arguments for vcftools as returned by |
indels |
what to do with indels; "keep" leaves them in, "remove" removes them, and "only" discards everything but indels. |
verbose |
print stdout from vcftools? |
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