obs.sumstat.ngs: Observed summary statistics for nexgen data

In gehara/PipeMaster: Building and Simulating Coalescent models.

Observed summary statistics for nexgen data

Description

This function calculates the observed summary statistics from an empirical data. This summary statistics are the same as those simulated by the sim.msABC.sumstat function. It is optimized for nexgen data.

Usage

obs.sumstat.ngs(
  model = NULL,
  path.to.fasta,
  pop.assign,
  moments = F,
  msABC.call = get.msABC()
)

Arguments

model	A model object built by the main.menu function. Any model with the same number of populations of your empirical data will work. This is just to build the sumstats names correctly.
path.to.fasta	Path to the folder containing all fastas to be included in the calculation. Invariable sites must be included in the fasta alignments. Invariable loci must also be included. Alignments must contain phased data.
pop.assign	A two-column data frame with sample names in the first column and the corresponding population membership preferably as numbers in the second column (If you have a single population the numbers wont matter). The numbers should match the population number in the model object.
msABC.call	String. Path to the msABC executable. msABC binaries for Mac's and Linux are included in the package and should work in most computers. There is no need to change that unless you want to compile the program yourself and point the function to it.

Value

A table containing the observed summary stats.

Note

This function does not work on Windows systems.

Author(s)

Marcelo Gehara

gehara/PipeMaster documentation built on Feb. 4, 2024, 8:11 a.m.