callCIN: Call Chromosomal Instability

View source: R/callCIN.R

callCINR 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))


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