SampleGenoOFWithMs: Sample ancestral population with ms 2 island model. Then...

In bcm-uga/TESS3_encho_sen: Inference of Spatial Population Genetic Structure

Sample ancestral population with ms 2 island model. Then admixe ancestral population along a longitudinal gradient.

Description

Sample ancestral population with ms 2 island model. Then admixe ancestral population along a longitudinal gradient.

Usage

SampleGenoOFWithMs(n, nsites.neutral, nsites.selected, crossover.proba,
  m.neutral, m.selected, mutation.rate.per.site, N0 = 10^6, k = 0.5,
  min.maf = 0.05, plot.debug = FALSE, tess3.ms = getOption("tess3.ms"))

Arguments

n	number of indivudual to sample
nsites.neutral	number of site between which recombination occur for neutral loci
nsites.selected	number of site between which recombination occur for selected loci
crossover.proba	corss-over probability between adjacent site per generation
m.neutral	migration rate for neutral loci
m.selected	migration rate for selected loci
mutation.rate.per.site	mutation rate per site
N0	population size
k	TODOC
min.maf	the locus with a maf less than this parameter are removed
plot.debug	if TRUE plot at different stage of the simulation
tess3.ms	ms binary path.

Value

TODOC

Examples

# tess3.ms <- "~/BiocompSoftware/msdir/ms"
# n <- 200
# K <- 2
# ploidy <- 1
# data.list <- SampleGenoOFWithMs(n = n,
#                              nsites.neutral = 100000,
#                              nsites.selected = 1000,
#                              crossover.proba = 0.25 * 10 ^ -8,
#                              m.neutral = 0.25 * 10 ^ -6,
#                              m.selected = 0.25 * 10 ^ -7,
#                              mutation.rate.per.site = 0.25 * 10 ^ -8,
#                              N0 = 10 ^ 6,
#                              k = 0.5,
#                              min.maf = 0.05,
#                              plot.debug = TRUE)

bcm-uga/TESS3_encho_sen documentation built on June 30, 2023, 3:08 a.m.