genind2bgc: Generate inputs for BGC from genind object. Does not use...

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

Generate inputs for BGC from genind object. Does not use genotype uncertainty.

Description

This function parses a genind object to create input data frames for running genomic cline analysis in BGC. It writes the appropriate output files as: <prefix>_p0in.txt, <prefix>_p1in.txt, and <prefix>_admixedin.txt

Usage

genind2bgc(
  gen,
  p1,
  p2,
  admix,
  missingPerLoc = 0.5,
  missingPerInd = 0.5,
  subset = NULL,
  drop = TRUE,
  prefix = "bgc"
)

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
prefix	A string giving the prefix for bgc input file names

Examples

bgc_input <- genind2bgc(genind, p1=c("PopA", "PopB"),
                                        p2="PopC", admix=c("PopD1", "PopD2"))

bgc_input <- genind2bgc(genind, p1=c("PopA", "PopB"),
                                        p2="PopC", admix=c("PopD1", "PopD2"),
                                        missingPerInd=0.75, missingPerLoc=0.25)

bgc_input <- genind2bgc(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.