setAlleleMats: Functions related to allele model Set allele count matrices,...

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

Description

Functions related to allele model Set allele count matrices, creates in-silico pooled single cells as bulk reference if none provided

Usage

setAlleleMats(r.init, n.sc.init, l.init = NULL, n.bulk.init = NULL,
  filter = TRUE, het.deviance.threshold = 0.05, min.cell = 3,
  n.cores = 1, verbose = TRUE)

Arguments

r.init	SNP site alternate allele count matrix for single cells
n.sc.init	SNP site coverage count matrix for single cells
l.init	SNP site alternate allele counts for bulk reference. If NULL, in silico bulk will be created from single cells.
n.bulk.init	SNP site coverage counts for bulk reference. If NULL, in silico bulk will be created from single cells.
filter	Whether to filter SNPs to only putative hterozygous SNPs based on the het.deviance.threshold
het.deviance.threshold	Deviation from expected 0.5 heterozygous fraction
min.cell	Minimum number of cells a SNP must have coverage observed in
n.cores	Number of cores
verbose	Verbosity

Examples

data(r)
data(cov.sc)
allele.mats <- setAlleleMats(r, cov.sc)

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