readAffyCytoScan {rCGH} | R Documentation

## Affymetrix CytoScanHD `"rCGH-cytoScan"` Constructor

### Description

A constructor function which takes an Affymetrix cytoScanHD cychp.txt (or cnchp.txt) file as input, possibly in a compressed format (.bz2 or .gz).
These files are exported from Chromosome Analysis Suite (ChAS) or Affymetrix Power Tools (see `References` section).

### Usage

    readAffyCytoScan(filePath, sampleName=NA, labName=NA,
        useProbes=c("snp", "cn", "all"), genome = c("hg19", "hg18", "hg38"),
        ploidy = 2, verbose=TRUE)

### Arguments

`filePath` | : string. A path to an Affymetrix cytoScanHD cychp.txt (or cnchp.txt) file.
`sampleName` | : string. A sample Id. Optional.
`labName` | : string. A lab Id. Optional.
`useProbes` | : character. What probes to consider. Possible choices are SNP probes only ("snp", default), CN probes only ("cn"), or all the probes ("all").
`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

When available in the file preambule, several array information will be stored in `Object@info`: scanning date, grid version,...
Any other useful item can be stored using `setInfo`.

### Value

An object of class `"rCGH"`

### Author(s)

Frederic Commo

### References

Affymetrix Power Tools

### See Also

`readAgilent`, `readAffySNP6`, `readGeneric`, `readAffyOncoScan`, `setInfo`, `getInfo`

### Examples

    filePath <- system.file("extdata", "Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2",
        package = "rCGH")
    cgh <- readAffyCytoScan(filePath, sampleName = "AffyScHD")
    cgh

[Package rCGH version 1.8.1 Index]