countAlleles: Mapping alleles to genes

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Mapping alleles to genes

Description

Make a data frame to summarise genes, alleles and allele frequencies.

Usage

countAlleles(pam.genes, pam.alleles, patterns = NULL, pat.sizes = NULL)

Arguments

pam.genes	a compiled matrix showing allele calls across isolates, where extended allele IDs have been assigned
pam.alleles	a presence-absence matrix of alleles, which is derived from the matrix pam.genes.
patterns	(optional) a data frame consisting of two columns: allele and pattern ID
pat.sizes	(optional) a two-column data frame (pattern and size) for the number of alleles per pattern

Author(s)

Yu Wan ([e-mail])

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.