importCoreGenomeSNPs: Import genotypes of core-genome SNPs

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

Import genotypes of core-genome SNPs

Description

Read the SNP table usually produced by the parseSNPtable.py of RedDog (https://github.com/katholt/RedDog). The function also compresses the SNP matrix into a pattern matrix. Notice it is the user's responsibility to ensure the input SNP table only contains 100

Usage

importCoreGenomeSNPs(
  snps,
  snps.delim = ",",
  pos.col = "Pos",
  ref.col = "Ref",
  replace.ref = NULL,
  min.mac = 1,
  ingroup = NULL,
  outliers = NULL,
  G.file = "",
  annots.file = "",
  skip = TRUE
)

Arguments

snps	either a path to the SNP table or a list generated by this function previously
snps.delim	a single character for the delimiter in the SNP table to be imported
pos.col	either a name or an index of the column for SNP positions
ref.col	(optional) A string specifying the column for SNPs of the reference genome.
replace.ref	Replace the column name specified by ref.col with this argument when ref.col is found amonst column names. Such a column is seen in the SNP table created using RedDog. A user may want to substitute it with a genuine strain name to match the reference isolate in the SNP matrix with that in the genetic and allelic matrices.
min.mac	the minimal number of times that each minor allele occurs in the population (with outlier isolates excluded) min.mac = 1: no filter of SNPs by the minor allele count (MAC) is applied. min.mac = 2: the filter is applied to remove any isolate-specific SNPs. min.mac > 2: the filter is applied for other purposes.
ingroup	a character vector of isolate names to be included in the SNP matrix
outliers	a character vector of names for outlier isolates (to be excluded from the SNP matrix)
G.file	file path of a bimbam-formatted genotype matrix (G). Keep it an empty character ("" by default) to prevent the function from writing this genotype matrix to the hard disk.
annots.file	file path of bimbam-formatted SNP annotations. Keep it "" to prevent the function from writing SNP annotations to the hard disk.
skip	whether to skip overwriting existing output files.

Author(s)

Yu Wan ([e-mail])

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