rCGH (version 1.2.2)

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"), genome = c("hg19", "hg18", "hg38"),
    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.

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

http://www.affymetrix.com/estore/partners_programs/programs/developer/tools/powertools.affx{Affymetrix Power Tools}

See Also

readAgilent, readAffySNP6, readGeneric, setInfo, getInfo

Examples

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