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

In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

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"),
    ploidy = 2, 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.
ploidy	: numeric. A priori ploidy 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, readAffyCytoScan, readGeneric, readAffyOncoScan, setInfo, getInfo

Examples

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

rCGH documentation built on Nov. 8, 2020, 8:30 p.m.