countAllelesPerGeneByCountry: Count each gene per country using their alleles

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

Count each gene per country using their alleles

Description

This function cares any alleles.

Usage

countAllelesPerGeneByCountry(sam, mapping, gm, nul = NA)

Arguments

sam	A data frame of sample information. Required columns: Strain, Country, Year_low and Year_up.
mapping	A data frame in the output of lmm or findPhysLink.
gm	Gene content matrix. Its column names must match the gene names in the mapping data frame.
nul	A value for zero counts. It can be zero definitely, but setting it to NA makes it easier to draw a heat map.

Author(s)

Yu Wan ([e-mail])

Examples

cc <- countAllelesPerGeneByCountry(sam = sam, mapping = assoc$mapping, gm = assoc$genes$all, nul = -35)

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