isHetAlt: Alternate helper function to determine heterzogosity at a...

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Alternate helper function to determine heterzogosity at a position from allele counts. Returns TRUE for heterozygous SNPs, FALSE otherwise based on coverage. If only reads are recorded from reference allele, then SNP is automatically classified as homozygous. If reads from both alleles or just the alternate allele are recorded, then the hypothesis test is applied

Usage

isHetAlt(cov, t = 1e-08)

Arguments

cov	vector of allele counts and coverage for a putative heterozygous SNP
t	threshold for hypothesis testing for heterozygosity, default 1e-8 (Illumina sequencing error rate)

Value

Boolean - TRUE for heterozygous, FALSE for homozygous

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.