runIntrogress: Functions to run INTROGRESS and correlate genomic clines X...

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

Functions to run INTROGRESS and correlate genomic clines X environment

Description

These functions run INTROGRESS and generate genomic clines. The genomic clines are then correlated with the raster values at each sampling locality for the raster layers determined to be the best predictors for species distributions in MAXENT. See ?prepare_rasters, ?partition_raster_bg, ?runENMeval, ?summarize_ENMeval, and ?extractPointValues.

Usage

runIntrogress(
  p1.file,
  p2.file,
  admix.file,
  loci.file,
  clineLabels = c("P1", "Het", "P2"),
  minDelt = 0.8,
  prefix = "population1",
  outputDIR = "./plots",
  showPLOTS = FALSE,
  sep = "\t",
  pop.id = FALSE,
  ind.id = FALSE,
  fixed = FALSE
)

Arguments

p1.file	Character string; File path for INTROGRESS p1 input file
p2.file	Character string; File path for INTROGRESS p2 input file
admix.file	Character string; File path for INTROGRESS admixed file
loci.file	Character string; File path for INTROGRESS loci file
clineLabels	Character vector of length == 3 for c(P1, Het, P2) populations
minDelt	Numeric; Minimum allele frequency delta to retain loci for INTROGRESS
prefix	Character string; Population prefix for input and output files
outputDIR	Character string; File path for INTROGRESS output
showPLOTS	Boolean; Whether to print the plots to the screen
sep	Character string; Column delimiter for INTROGRESS input files
pop.id	Boolean; Value for INTROGRESS parameter pop.id. See ?prepare.data in introgress R pacakge
ind.id	Boolean; Value for INTROGRESS parameter ind.id See ?prepare.data in introgress R package
fixed	Boolean; TRUE if input data are fixed SNPs

Details

Function to run INTROGRESS

Value

List object containing genomic cline output

Examples

eatt <- runIntrogress(p1.file = "EATT_p1data.txt",
                      p2.file = "EATT_p2data.txt",
                      admix.file = "EATT_admix.txt",
                      loci.file = "EATT_loci.txt",
                      clineLabels = c("EA", "Het", "TT")
                      minDelt = 0.8,
                      prefix = "eatt",
                      outputDIR = "./introgress_plots",
                      sep = "\t",
                      pop.id = FALSE,
                      ind.id = FALSE,
                      fixed = FALSE)

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