extractPED: Extract PED files from gds

In sa-lee/moimix: Estimating mulitplicity of infection from high-throughput sequencing data

Description

Extract PED files from gds

Usage

extractPED(gdsfile, moi.estimates = NULL, use.hets = FALSE, outfile = NULL)

Arguments

gdsfile	a SeqVarGDSClass object
moi.estimates	a vector of MOI values obtained by binommix for each sample. DEFAULT NULL
use.hets	FALSE include heterozygote genotypes
outfile	prefix of PLINK files for output (default NULL)

Details

This function writes a plink .ped and .map file for a given gdsfile. If moi.estimates is set then use.hets is redundant. It will set the sex in each the ped file to 2 if MOI > 1 and set heterozygote genotypes to missing for MOI = 1 calls. This is for use in isoRelate. If the use.hets option is true the genotypes are used as is, other wise heterzygotes are set to missing. This function is slow if there are a large number of variants in the GDS file.

sa-lee/moimix documentation built on April 23, 2020, 10:32 a.m.