readAffySNP6: Affymetrix SNP6 `"rCGH-SNP6"` Constructor

Description

A constructor function which takes an Affymetrix SNP6 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 (APT) (see the References section).

Usage

readAffySNP6(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 SNP6 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}

Examples

Run this code

filePath <- system.file("extdata", "Affy_snp6_cnchp.txt.bz2", package = "rCGH")
cgh <- readAffySNP6(filePath, sampleName = "AffySNP6")
cgh

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