CopyNumberSet-methods {oligoClasses} | R Documentation |
Accessors and CopyNumberSet
copyNumber(object, ...) cnConfidence(object) copyNumber(object) <- value cnConfidence(object) <- value
object |
|
... |
Ignored for |
value |
matrix |
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.
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)