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Last data update: 2014.03.03

R: Calculate the posterior probability for integer copy numbers.

posteriorProbability

R Documentation

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(crlmm)
Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: preprocessCore
Welcome to crlmm version 1.30.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/crlmm/posteriorProbability.Rd_%03d_medium.png", width=480, height=480)
> ### Name: posteriorProbability
> ### Title: Calculate the posterior probability for integer copy numbers.
> ### Aliases: posteriorProbability posteriorProbability,CNSet-method
> ### Keywords: array
> 
> ### ** Examples
> 
> data(cnSetExample)
> pr <- predictionRegion(cnSetExample, copyNumber=0:4)
> pp <- posteriorProbability(cnSetExample, predictRegion=pr)
> dim(pp)
Features  Samples          
   15000        2        5 
> 
> ## multiple batches
> data(cnSetExample2)
> pr <- predictionRegion(cnSetExample2, copyNumber=0:4)
> pp <- posteriorProbability(cnSetExample2, predictRegion=pr)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>