`multiPopsizeFileFromPsmc`¶

For multiple population model in arg-sample, create popsize file using one representative PSMC result file per population

Description¶

For multiple population model in arg-sample, create popsize file using one representative PSMC result file per population

Usage¶

multiPopsizeFileFromPsmc(psmcFiles, ages = NULL, ntimes = 20,
  delta = 0.01, maxTime = 1e+06, mu = 1.4e-08, s = 100,
  outfile = NULL)

Arguments¶

Argument	Description
`psmcFiles`	A list with length = number of populations. Each element should be a character string giving the file path of PSMC result for a population, or can be a single numeric value for constant size population (giving diploid population size)
`ages`	(Used for ancient samples) A numeric vector of same length as psmcFiles. Each value represents the age in generations of the sample used in PSMC.
`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
`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 columns: population, time, popsizse (invisibly if outfile is not NUL)

Note¶

Note that this function is for multiple-population model of arg-sample, which is still experimental. Most users will want a single vector of population sizes, using the function psmcToPopsize function instead.