getPhi: Summary Statistics to estimate recombination from PhiPack

In PhHermann/LDJump: Estimating Variable Recombination Rates from Population Genetic Data

Description

This functions calls the PhiPack software and extracts the four summary statistics MaxChi, NSS and the mean and the variance of Phi.

Usage

getPhi(seqName, pathPhi, out, rm)

Arguments

seqName	A character string containing the full path and the name of the sequence file in fasta of vcf format. It is necessary to add the extension ("fileName.fa", "fileName.fasta", "fileName.vcf") in order to run LDJump. In case that format equals to DNABin the seqName equals to the name of the DNABin-object (without any extension).
pathPhi	A character string containing the path to PhiPack. This path and the installation of PhiPack is necessary for the computation of the package.
out	an optional character string: by default an empty string "". Can be set to any user-defined string in order to rename all output files used within LDJump and PhiPack. This parameter enables to run LDJump from the same directory without creating interfering files in the working directory.
rm	an optional logical value: by default TRUE such that the internally produced fasta file as well as the output file are deleted shortly before finishing the function. This option is added in order to avoid deleting a file of interest when running the function gethi outside LDJump.

Value

A vector is returned containing the four summary statistics MaxChi, NSS and the mean and the variance of Phi.

References

Bruen, T., Phillipe, H. and Bryant, D. 2006. A quick and robust statistical test to detect the presence of recombination. Genetics 172, 2665–2681.

See Also

LDJump, vcfR_to_fasta, get_smuce

Examples

## The function is currently defined as
##getPhi(seqName = seqName, pathPhi = pathPhi)

PhHermann/LDJump documentation built on Nov. 16, 2019, 12:53 p.m.