HoneyBADGER_calcAlleleCnvProb: Calculate posterior probability of CNVs using allele data

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

Description

Calculate posterior probability of CNVs using allele data

Arguments

r.sub	Optional matrix of alt allele count in single cells. If not provided, internal r.sc matrix is used.
n.sub	Optional matrix of site coverage count in single cells. If not provided, internal n.sc matrix is used.
l.sub	Optional vector of alt allele count in pooled single cells or bulk. If not provided, internal l vector is used.
n.bulk.sub	Optional vector of site coverage count in pooled single cells or bulk. If not provided, internal n.bulk vector is used.
region	GenomicRanges region of interest such as expected CNV boundaries.
filter	Boolean for whether to filter out SNP sites with no coverage. (default: TRUE)
pe	Effective error rate to capture error from sequencing, etc. (default: 0.01)
mono	Rate of mono-allelic expression. (default: 0.7)
n.iter	Number of iterations in MCMC. (default: 1000)
quiet	Boolean of whether to suppress progress bar. (default: TRUE)
verbose	Verbosity(default: FALSE)

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