isHet: Helper function to determine heterzogosity at a position from...

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

Description

Helper function to determine heterzogosity at a position from allele counts Returns TRUE for heterozygous SNPs, FALSE otherwise based on coverage If reads are recorded from only one of reference or alternate allele, then it is automakically classified as homozygous If reads from both alleles are recorded, then we adopt a null hypothesis that the number of minor allele reads sequenced is distributed according to Binomial(p = 0.5, n), where n is the total read depth at that position. SNPs at which the null hypothesis p = 0.5 was rejected were classified as homozygous, while the remainder were classified as heterozygous.

Usage

isHet(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.