CopyNumberSet-methods {oligoClasses} | R Documentation

## Methods for class CopyNumberSet.

### Description

Accessors and CopyNumberSet

### Usage

    copyNumber(object, ...)
    cnConfidence(object)
    copyNumber(object) <- value
    cnConfidence(object) <- value

### Arguments

`object` | `CopyNumberSet` object or derived class
`...` | Ignored for `CopyNumberSet` and `oligoSnpSet`.
`value` | matrix

### Value

`copyNumber` returns a matrix of copy number estimates or relative copy number estimates. Since the copy number estimates are stored as integers (copy number * 100), the matrix returned by the `copyNumber` accessor will need to be divided by a factor of 100 to transform the measurements back to the original copy number scale.

`cnConfidence` returns a matrix of confidence scores for the copy number estimates. These are also represented as integers and will require a back-transformation to the original scale.

### Examples

    	library(Biobase)
    	data(locusLevelData)
    	path <- system.file("extdata", package="oligoClasses")
    	fd <- readRDS(file.path(path, "genomeAnnotatedDataFrameExample.rds"))
    	## the following command creates an 'oligoSnpSet' object, storing
    	## an integer representation of the log2 copy number in the 'copyNumber' element
    	## of the assayData.  Genotype calls and genotype confidence scores are also stored
    	## in the assayData.
    	oligoSet <- new("oligoSnpSet",
    			copyNumber=integerMatrix(log2(locusLevelData[["copynumber"]]/100), 100),
    			call=locusLevelData[["genotypes"]],
    			callProbability=integerMatrix(locusLevelData[["crlmmConfidence"]], 1),
    			annotation=locusLevelData[["platform"]],
    			featureData=fd,
    			genome="hg19")

    	## There are several accessors for the oligoSnpSet class.
    	icn <- copyNumber(oligoSet)
    	range(icn) ## integer scale
    	lcn <- icn/100
    	range(lcn) ## log2 copy number

    	## confidence scores for the genotypes are also represented on an integer scale
    	ipr <- snpCallProbability(oligoSet)
    	range(ipr) ## integer scale

    	## for genotype confidence scores, the helper function i2p
    	## converts back to a probability scale
    	pr <- i2p(ipr)
    	range(pr)

    	## The helper function confs is a shortcut, extracting the
    	## integer-based confidence scores and transforming to the
    	## probability scale
    	pr2 <- confs(oligoSet)
    	all.equal(pr, pr2)

    	## To extract information on the annotation of the SNPs, one can use
    	position(oligoSet)
    	chromosome(oligoSet)
    	## the position and chromosome coordinates were extracted from build hg19
    	genomeBuild(oligoSet)

[Package oligoClasses version 1.56.0 Index]