readAffyOncoScan: Affymetrix OncoScan '"rCGH-oncoScan"' Constructor
In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

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

`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.

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.

An object of class "rCGH"

Frederic Commo

Affymetrix Power Tools

readAgilent, readAffySNP6, readGeneric, readAffyCytoScan, setInfo, getInfo

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