PSCBS (version 0.68.0)

findNeutralCopyNumberState: Call segments to be copy neutral based on allelic imbalance calls and total copy number estimates

Description

Call segments to be copy neutral based on allelic imbalance calls and total copy number estimates.

Usage

# S3 method for default
findNeutralCopyNumberState(C, isAI, weights=NULL, ..., minDensity=1e-10,
  flavor=c("firstPeak", "maxPeak"), verbose=FALSE)

Value

A logical

vector of "neutral copy number state" calls.

Arguments

C

A numeric vector of region-level total copy number estimates.

isAI

A logical vector of "allelic imbalance" calls.

weights

An optional numeric vector of non-negative weights.

...

Further arguments to be passed to the density estimation function.

minDensity

A numeric value, below which density peaks are discarded.

flavor

A character string specifying how to identify the mode of the AB segments.

verbose

If TRUE, extra information is output.

Author

Pierre Neuvial, Henrik Bengtsson