fsc.loadScenario: Load skeleSim scenario parameters for fastsimcoal

Description Usage Arguments Value Note

View source: R/fsc.loadScenario.R

Description

Load skeleSim scenario parameters for fastsimcoal

Usage

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fsc.loadScenario(num.pops, pop.size, sample.size, mut.rate, migration = NULL,
  sample.times = NULL, growth.rate = NULL, locus.type = c("dna", "msat",
  "snp"), sequence.length = NULL, num.loci = NULL, transition.rate = NULL,
  gsm.param = NULL, range.constraint = NULL, recomb.rate = NULL,
  chromosome = NULL, num.chrom = NULL, num.gen = NULL,
  source.deme = NULL, sink.deme = NULL, prop.migrants = NULL,
  new.sink.size = NULL, new.sink.growth = NULL, new.mig.mat = NULL,
  fastsimcoal.exec = "fsc252")

Arguments

num.pops

number of populations.

pop.size

a vector giving size of each populaiton.

sample.size

a vector giving the number of samples to take from each population.

mut.rate

dna, msat: per base pair or locus mutation rate.

migration

a num.pop x num.pop matrix or list of matrices giving the migration rates between each population.

sample.times

a vector giving the number of generations in the past at which samples are taken.

growth.rate

a vector giving the growth rate of each population.

locus.type

a character representation of what type of marker to simulate. Can be "dna", "msat", or "snp".

sequence.length

dna: number of DNA base pairs to use.

num.loci

msat, snp: number of loci to simulate.

transition.rate

dna: fraction of substitutions that are transitions.

gsm.param

msat: Value of the geometric parameter for a Generalized Stepwise Mutation (GSM) model. This value represents the proportion of mutations that will change the allele size by more than one step. Values between 0 and 1 are required. A value of 0 is for a strict Stepwise Mutation Model (SMM).

range.constraint

msat: Range constraint (number of different alleles allowed). A value of 0 means no range constraint.

recomb.rate

recombination rate between adjacent markers.

chromosome

number or character identifying which chromosome the marker is on.

num.chrom

a value giving the number of chromosomes that the locus.params marker specifications should be copied for. If NULL, then chromosome assignment is taken from the chromosome column in locus.params. Any non-NULL integer will cause the chromosome column to be ignored.

num.gen

Number of generations, t, before present at which the historical event happened.

source.deme

Source deme (the first listed deme has index 0)

sink.deme

Sink deme

prop.migrants

Expected proportion of migrants to move from source to sink.

new.sink.size

New size for the sink deme, relative to its size at generation t.

new.sink.growth

New growth rate for the sink deme.

new.mig.mat

New migration matrix to be used further back in time.

fastsimcoal.exec

executable

Value

a scenario.params object to be loaded into a list in the scenarios slot of a skeleSim.params object.

Note

Vectors for pop.size, sample.size, sample.times, and growth.rate will be expanded/recycled to ensure they are as long as num.pops.

Depending on the choice of locus.type, values for some arguments may be ignored. See argument list above for which arguments are applicable to which locus.type.


skeleSim documentation built on Nov. 28, 2017, 1:05 a.m.