getHetRate: Helper function to get het rate from allele counts at a list...

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

Description

Helper function to get het rate from allele counts at a list of common variant SNPs

Usage

getHetRate(snpSummary, t = 1e-08, alt = FALSE)

Arguments

snpSummary	data frame of common variant SNPs and their allele counts and coverage
t	threshold for hypothesis testing for heterozygosity, default 1e-8 (Illumina sequencing error rate)
alt	Boolean of whether or not to use alternate het filter

Value

hetRate percentage of heterozygous SNPs in the input data frame

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