Plot BAF distributions per allele specific state

Plot BAF distributions per allele specific state

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

if (FALSE) {
data("haplotypes")
data("CNbins")
haplotypes <- format_haplotypes_dlp(haplotypes, CNbins)
hscn <- callHaplotypeSpecificCN(CNbins, haplotypes, likelihood = "binomial")
plotBAFperstate(hscn, genes = "MYC")
}