ppgrid: ppgrid

In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

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 = 1,
  return.nll = FALSE
)

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
purity.min	min purity value allowed
purity.max	max purity value allowed
ploidy.step	grid length of ploidy values
purity.step	grid length of purity values
ploidy.min	min ploidy value allowed
ploidy.max	max ploidy value allowed
plot	whether to plot the results to file
verbose	print intermediate outputs
mc.cores	integer number of cores to use (default 1)
return.all	return the log likelihood matrix

Value

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

mskilab/casereport documentation built on Oct. 19, 2022, 3 a.m.