findNeutralCopyNumberState: Call segments to be copy neutral based on allelic imbalance...

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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

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

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.

Value

A logical vector of "neutral copy number state" calls.

Author(s)

Pierre Neuvial, Henrik Bengtsson

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.