importGeneticPAM: Import the genetic presence/absence (p/a) matrix

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

Import the genetic presence/absence (p/a) matrix

Description

This function reads the genetic presence-absence matrix and returns a list of relevant matrices. It automatically matches isolates to those in the SNP matrix.

Usage

importGeneticPAM(
  pam,
  pam.delim = "\t",
  outliers = NULL,
  min.count = 1,
  genes.rm = NULL,
  sample.order = NULL
)

Arguments

pam	Expect pam to be "modified_allele_matrix.txt" produced by the cdhitFormatter pipeline. First column of pam consists of isolate names. Other columns: presence/absence profile of every gene The genetic PAM may contain more alleles than the allelic PAM does, because the latter applies a more stringent criterion to filter data.
pam.delim	a single character for the delimiter in the text file of the genetic PAM
outliers	a vector of isolate names to be excluded from rows of the PAM
min.count	the minimal number of times that a gene occurs in all isolates excluding outliers By default, only genes that do not occur at all are removed (min.count = 1). When min.count = 2, isolate-specific genes are removed as well.
genes.rm	a vector of gene names to be excluded from columns of the genetic PAM.
sample.order	a vector of isolate names for the PAM to be matched with. It can be used to filter the genetic PAM for in-group isolates.

Author(s)

Yu Wan ([e-mail])

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