callAlterations: Calling of amplifications and deletions

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Calling of amplifications and deletions

Description

Function to extract major copy number alterations from a runAbsoluteCN return object.

Usage

callAlterations(
  res,
  id = 1,
  cutoffs = c(0.5, 6, 7),
  log.ratio.cutoffs = c(-0.9, 0.9),
  failed = NULL,
  all.genes = FALSE
)

Arguments

res	Return object of the runAbsoluteCN function.
id	Candidate solutions to be used. id=1 will use the maximum likelihood (or curated) solution.
cutoffs	Copy numbers cutoffs to call losses, focal amplifications and broad amplifications.
log.ratio.cutoffs	Copy numbers log-ratio cutoffs to call losses and amplifications in failed samples.
failed	Indicates whether sample was failed. If NULL, use available annotation, which can be set in the curation file.
all.genes	If FALSE, then only return amplifications and deletions passing the thresholds.

Value

A data.frame with gene-level amplification and deletion calls.

Author(s)

Markus Riester

See Also

runAbsoluteCN

Examples

data(purecn.example.output)
callAlterations(purecn.example.output)
callAlterations(purecn.example.output, all.genes=TRUE)["ESR2",]

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.