subset_variants {BeviMed}

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

Integer vector with a length equalling the number of individuals or length 1 (in which case the given value is used for all individuals) giving the minimum number of alleles at pathogenic variant sites each individual requires in order to classify as having a ‘pathogenic allele configuration’. Thus, this parameter encodes the mode of inheritance. For instance, setting this parameter to 1 corresponds to dominant inheritance. 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 ensure sex is accounted for 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