filter_variants: Filter Variants from Allele Count

In andremrsantos/htspop: High-Troughput Sequencing Population Genetics Statistics

Description

Implements common strategies to filter variants of an allele frequency matrix, including complete_variants, which exclude variants with missing genotype, and informative_variants, which excludes variants were allgroups are reference or alternative homozygous and keeping only informative sites. These functions return a boolean vector of the subset and can also be used with filter_variants to return the subsetted allele count or frequency matrix.

Usage

filter_variants(x, fn, cols = NULL)

complete_variants(x, cols = NULL)

informative_variants(x, cols = NULL)

Arguments

x	A allele count or frequency matrix to be filtered.
cols	A vector indicating the subset of columns considered.

andremrsantos/htspop documentation built on May 14, 2020, 11:40 a.m.