callCIN: Call Chromosomal Instability

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

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))

lima1/PureCN documentation built on April 24, 2024, 8:23 p.m.