readAffyOncoScan {rCGH}R Documentation

Affymetrix OncoScan "rCGH-oncoScan" Constructor

Description

A constructor function which takes an Affymetrix oncoScan tabulated file as input, possibly in a compressed format (.bz2 or .gz).
This can be either a 'ProbeSets,CopyNumber.tsv' alone, or merged with its corresponding 'ProbeSets,AllelicData.tsv' file. See the details section.

Usage

readAffyOncoScan(filePath, sampleName=NA, labName=NA,
    genome = c("hg19", "hg18", "hg38"),
    ploidy = 2, verbose=TRUE)

Arguments

filePath

: string. A path to an Affymetrix .tsv file. See details.

sampleName

: string. A sample Id. Optional.

labName

: string. A lab Id. Optional.

genome

: string. The genome build to use. Supported genomes are hg18, hg19 (default), and hg38.

ploidy

: numeric. A priori plody value, when known, to adjust the estimation of copy numbers. Default is 2.

verbose

: logical. When TRUE (default), progress is printed.

Details

The Affymetrix Power Tools apt-copynumber-onco-ssa script produces 2 files: 'ProbeSets,CopyNumber.tsv' and 'ProbeSets,AllelicData.tsv'. Merging these 2 files may produce a unique file containing both probes Log2Ratio and AllelicDifference.

Value

An object of class "rCGH"

Author(s)

Frederic Commo

References

Affymetrix Power Tools

See Also

readAgilent, readAffySNP6, readGeneric, readAffyCytoScan, setInfo, getInfo

Examples


# Just a toy file
filePath <- system.file("extdata", "oncoscan.tsv.bz2", package = "rCGH")
cgh <- readAffyOncoScan(filePath, sampleName = "AffyOncoScan")
cgh
[Package rCGH version 1.8.1 Index]