plotBAFperstate: Plot BAF distributions per allele specific state

In shahcompbio/signals: Single Cell Genomes with Allele Specificity

Plot BAF distributions per allele specific state

Description

Plot BAF distributions per allele specific state

Usage

plotBAFperstate(
  cn,
  minpts = 250,
  minfrac = 0.01,
  maxstate = 10,
  dens_adjust = 2,
  mincounts = 6
)

Arguments

cn	Either a hscn object or a single cell allele specific copy number dataframe with the following columns: 'cell_id', 'chr', 'start', 'end', 'state', 'copy', 'BAF'
minpts	minimum number of points to include default = 250
minfrac	states that are present below this fraction will be removed, default = 0.01
maxstate	States with total copy number > maxstate will be removed, default = 10
dens_adjust	density adjustment factor in the violin plots
mincounts	filter out bins < mincounts from plotting, default = 6

Examples

## Not run: 
data("haplotypes")
data("CNbins")
haplotypes <- format_haplotypes_dlp(haplotypes, CNbins)
hscn <- callHaplotypeSpecificCN(CNbins, haplotypes, likelihood = "binomial")
plotBAFperstate(hscn, genes = "MYC")

## End(Not run)

shahcompbio/signals documentation built on Jan. 11, 2025, 2:20 a.m.