psmcToPopsize

Make a popsize file suitable for arg-sample from PSMC output

Description

Make a popsize file suitable for arg-sample from PSMC output

Usage

psmcToPopsize(psmcFile, ntimes = 20, delta = 0.01, maxTime = 2e+05,
  mu = 1.4e-08, s = 100, sampleAge = 0, outfile = NULL)

Arguments

Argument	Description
psmcFile	File with PSMC output
ntimes	Number of time points in arg-sample model
delta	arg-sample delta parameter
maxTime	maximum time point used in arg-sample
mu	mutation rate in mutations per base pair per generation
s	The bin size used in the fq2psmcfa command; the default in that program is 100
sampleAge	The age of the sample, in generations (For ancient samples)
outfile	If not NULL, path to write output popsize file. This file is suitable for use with the “–popsize-file” option in arg-sample.

Value

a data frame with time and popsize (invisibly if outfile is provided)