callAlterations: Calling of amplifications and deletions

View source: R/callAlterations.R

callAlterationsR Documentation

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.