callMajor: Get major allele calls for isolates from BAF matrix

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

Description

Extract major alleles from a GDS file using the non-reference allele frequency (NRAF) estimated from read counts directly. In the case of RAF = 0.5 we select the major allele randomly from Bernoulli distribution if use.hets is FALSE. Other wise hets are coded as 3. If get.nucleotides is TRUE a character matrix is retruned with the alleles coded, otherwise if use.hets the allele is coded as N. Missing genotype calls are coded as X.

Usage

callMajor(gdsfile, get.nucleotides = FALSE, use.hets = FALSE)

Arguments

gdsfile	a SeqVarGDSClass object
get.nucleotides	FALSE logical indicating whether to replace allele with nucleotide bases
use.hets	FALSE logical indicating whether to code hets sepeartely

Value

a binary matrix or character matrix containing reference and alternate alleles

bahlolab/moimix documentation built on April 16, 2020, 8:40 a.m.