mkFilterTSV: Making a guidance TSV file as an input for the physDist...

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

Making a guidance TSV file as an input for the physDist pipeline

Description

The function prints allele names of each strain when it has at least two alleles.

Usage

mkFilterTSV(
  allele.mat = NULL,
  pam.a = NULL,
  output = "targeted_isolates_alleles.tsv"
)

Arguments

allele.mat	A matrix in the output format of SRST2, which shows an allele per gene for each sample. This argument overrides pam.a. Row names of this matrix are sample names and column names are gene names. There must not be a column of sample names.
pam.a	A presence-absence matrix of alleles. It is an alternative to the allele.mat argument and it must not be a data frame. Row names of this matrix are sample names and column names are allele names. Again, there must not be a column of sample names.
output	Name of the output file Either allele.mat or pam.a is expected to be used as an input for this function.

Author(s)

Yu Wan ([e-mail])

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