posteriorProbability: Calculate the posterior probability for integer copy numbers.

In benilton/crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Calculate the posterior probability for integer copy numbers.

Description

Calculate the posterior probability for integer copy numbers using the bivariate normal prediction regions.

Usage

posteriorProbability(object, predictRegion, copyNumber = 0:4, w)

Arguments

object	A CNSet object.
predictRegion	A list containing the bivariate normal prediction region for each of the possible genotypes.
copyNumber	Integer vector.
w	numeric vector of prior probabilities for each of the copy number states. Must be the same length as copyNumber and sum to 1.

Details

This is currently under development.

Value

An array (features x samples x copy number)

Note

This is under development. Use at your own risk.

Author(s)

R. Scharpf

See Also

predictionRegion, genotypes

Examples

data(cnSetExample)
pr <- predictionRegion(cnSetExample, copyNumber=0:4)
pp <- posteriorProbability(cnSetExample, predictRegion=pr)
dim(pp)

## multiple batches
data(cnSetExample2)
pr <- predictionRegion(cnSetExample2, copyNumber=0:4)
pp <- posteriorProbability(cnSetExample2, predictRegion=pr)

benilton/crlmm documentation built on June 10, 2025, 8:13 p.m.