callAlterations {PureCN} | R 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",]

[Package PureCN version 2.0.2 Index]