callCIN {PureCN} | R Documentation

## Call Chromosomal Instability

### Description

This function provides detailed CIN information.

### Usage

    callCIN(
      res,
      id = 1,
      allele.specific = TRUE,
      reference.state = c("dominant", "normal")
    )

### Arguments

`res` | Return object of the `runAbsoluteCN` function.
`id` | Candidate solution to extract CIN from. `id=1` will use the maximum likelihood solution.
`allele.specific` | Use allele-specific or only total copy number for detecting abnormal regions. Copy-number neutral LOH would be ignored when this parameter is set to `FALSE`.
`reference.state` | Copy number regions different from the reference state are counted as abnormal. Default is `dominant` means the most common state. The other option is `normal`, which defines normal heterozygous, diploid as reference. The default is robust to errors in ploidy.

### Value

Returns `double(1)` with CIN value.

### Author(s)

Markus Riester

### See Also

`runAbsoluteCN`

### Examples

    data(purecn.example.output)
    head(callCIN(purecn.example.output))

[Package PureCN version 1.22.2 Index]