countAllelesPerCountry: Count alleles per country

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

Count alleles per country

Description

Count alleles per country

Usage

countAllelesPerCountry(
  alleles = NULL,
  sam,
  mapping,
  apam,
  nul = NA,
  freq = FALSE
)

Arguments

alleles	A character vector of allele names.
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.
apam	Allelic presence-absence matrix.
nul	A value for zero counts. It can be zero definitely, but setting it to NA makes it easier to draw a heat map.
freq	A logical argument determining if the allele frequency (in rather than allele count is returned.

Value

This function returns a list of two elements: count and mapping, when freq = FALSE, else, returns a list of three elements: freq, mapping and sample_size_country.

Author(s)

Yu Wan ([e-mail])

Examples

a_nat <- countAllelesPerCountry(alleles = nwk$V$allele, sam = sam, mapping = assoc$mapping, apam = assoc$alleles$A, nul = -30)

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