ppgrid: ppgrid

In mskilab/skitools: Various mskilab R utilties

ppgrid

Description

least squares grid search for purity and ploidy modes

Usage

ppgrid(
  segstats,
  allelic = FALSE,
  purity.min = 0.01,
  purity.max = 1,
  ploidy.step = 0.01,
  purity.step = 0.01,
  ploidy.min = 1.2,
  ploidy.max = 6,
  plot = F,
  verbose = F,
  mc.cores = 10
)

Arguments

segstats	GRanges object of intervals with meta data fields "mean" and "sd" (i.e. output of segstats function)
allelic	logical flag, if TRUE will also look for mean_high, sd_high, mean_low, sd_low variables and choose among top solutions from top copy number according to the best allelic fit
mc.cores	integer number of cores to use (default 1)

Value

data.frame with top purity and ploidy solutions and associated gamma and beta values, for use in downstream jbaMI

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.