HoneyBADGER_plotAlleleProfile: Plot allele profile

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

Description

Plot allele profile

Arguments

r.sub	SNP lesser allele count matrix for single cells. If NULL, object's r.maf will be used
n.sc.sub	SNP coverage count matrix for single cells. If NULL, object's n.sc will be used
l.sub	SNP lesser allele count matrix for bulk refernece. If NULL, object's l.maf will be used
n.bulk.sub	SNP coverage count matrix for bulk refernece. If NULL, object's n.bulk will be used
region	Limit plotting to particular GenomicRanges regions
chrs	Limit plotting to select chromosomes. Default autosomes only. (default: paste0('chr', c(1:22)))
setWidths	Set widths on chromosomes based on SNP density. Otherwise will be uniform.
cellOrder	Order of cells. Otherwise will be same order as in input matrix
filter	Remove sites with no coverage
returnPlot	Whether to return ggplot object
max.ps	Maximum point size for plot

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