getGenotypes: Import genotypes from GDS

In CMWbio/geaR: GDS Evolutionary Analysis in R

Import genotypes from GDS

Description

Imports genotypes across a locus into matrix

Usage

getGenotypes(
  GDS,
  locus = NULL,
  minSites = 0.5,
  raw = FALSE,
  ploidy = 2,
  pops = NULL,
  removeIndels = TRUE
)

Arguments

GDS	GDS object with variant data to import genotypes from
locus	GRanges Locus to import genotypes for
minSites	numeric minimum number of sites as a proportion of loci length
ploidy	numeric ploidy of sample
pops	tibble populaiton dataFrame
removeIndels	removes indels
nucleotide	logical Import RAW genotypes or nucleotides

Details

Authours: Chris Ward & Alastair Ludington Uses a GRanges locus to import genotypes, either nucleotide or RAW, from a GDS file

Value

A matrix of genotypes

CMWbio/geaR documentation built on April 22, 2023, 6:23 a.m.