subset_variants {BeviMed}R Documentation

Remove variants with no data for pathogenicity

Description

Subset an allele count matrix given a minimum allele count threshold for pathogenicity per individual so that only variants for which data relevant to pathogencity are retained. This is useful to apply before running bevimed as it reduces the size of the parameter space used in the inference.

Usage

subset_variants(G, min_ac = 1L, return_variants = FALSE)

Arguments

G

Integer matrix of variant counts per individual, one row per individual and one column per variant.

min_ac

Numeric vector of length the same as y or length 1 (in which case it is repeated to make it the same length as y) giving the minimum number of alleles at pathogenic variant sites each individual requires in order to classify as having a ‘pathogenic allele configuration’. If For example, 1 could correspond to hypothesis of dominant inheritance hypothesis. If there are differences in ploidy between individuals in the locus, it is necessary to set it on an sample level basis - e.g. to incorporate information about gender if the locus lies on the X chromosome.

return_variants

Logical value determining whether to return an integer vector of indices of retained variants or the subsetted allele count matrix


[Package BeviMed version 5.3 Index]