rCGH (version 1.0.0)

readAffyCytoScan: 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"), 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").

verbose

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

Value

An object of class "rCGH"

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.

References

Affymetrix Power Tools

See Also

readAgilent, readAffySNP6, setInfo, getInfo

Examples

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