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 1.16.0 Index]