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

Usage

plotAlleleProfile(r.maf, n.sc, l.maf, n.bulk, snps, region = NULL,
  chrs = paste0("chr", c(1:22)), widths = NULL, cellOrder = NULL,
  filter = FALSE, max.ps = 3, verbose = FALSE)

Arguments

r.maf	SNP lesser allele count matrix for single cells.
n.sc	SNP coverage count matrix for single cells.
l.maf	SNP lesser allele count matrix for bulk refernece.
n.bulk	SNP coverage count matrix for bulk refernece.
snps	SNP annotations
region	Limit plotting to particular GenomicRanges regions
chrs	Limit plotting to select chromosomes. Default autosomes only. (default: paste0('chr', c(1:22)))
widths	Widths of chromosomes in plot. If 'set' will depend on number of SNPs in region. Else will be equal.
cellOrder	Order of cells. If 'set' will be automatically ordered by clustering. Else will be same order as input.
filter	Remove sites with no coverage
max.ps	Maximum point size for plot.
verbose	Verbosity

Examples

data(r)
data(cov.sc)
allele.mats <- setAlleleMats(r, cov.sc)
plotAlleleProfile(allele.mats$r.maf, allele.mats$n.sc, 
    allele.mats$l.maf, allele.mats$n.bulk, allele.mats$snps, 
    widths=c(249250621, 243199373, 198022430, 191154276, 180915260, 
    171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 
    133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 
    78077248, 59128983, 63025520, 51304566, 48129895)/1e7) 

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