genind2introgress: Generate inputs for Introgress from genind object

In btmartin721/ClineHelpR: Parses and Plots BGC and INTROGRESS Output

Generate inputs for Introgress from genind object

Description

This function parses a genind object to create input data frames for running genomic cline analysis in the Introgress R package

Usage

genind2introgress(
  gen,
  p1,
  p2,
  admix,
  missingPerLoc = 0.5,
  missingPerInd = 0.5,
  subset = NULL,
  drop = TRUE,
  prefix = "introgress"
)

Arguments

gen	Genind object containing data for parental and admixed populations
p1	Character or vector containing population names for the p1 group
p2	Character or vector containing population names for the p2 group
admix	Character or vector containing population names for the admixed individuals
missingPerLoc	Proportion of missing genotypes allowed to retain a locus
missingPerInd	Proportion of missing genotypes allowed to retain an individual
subset	An optional parameter defining a number of loci to randomly retain
drop	Boolean value defining whether or not to remove monomorphic loci
prefix	Prefix for output Introgress files (default="introgress")

Examples

introgress_input <- genind2introgress(genind, p1=c("PopA", "PopB"),
                                        p2="PopC", admix=c("PopD1", "PopD2"))

introgress_input <- genind2introgress(genind, p1=c("PopA", "PopB"),
                                        p2="PopC", admix=c("PopD1", "PopD2"),
                                        missingPerInd=0.75, missingPerLoc=0.25,
                                        drop=TRUE)

introgress_input <- genind2introgress(genind, p1=c("PopA", "PopB"),
                                        p2="PopC", admix=c("PopD1", "PopD2"),
                                        subset=500)

btmartin721/ClineHelpR documentation built on Oct. 15, 2024, 5:05 a.m.