readAgilent: Agilent Dual-Color Hybridization '"rCGH-Agilent"'...
In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Description Usage Arguments Details Value Author(s) See Also Examples

A constructor function taking as input an Agilent FE .txt file, exported from Feature Extraction, possibly in a compressed format (.bz2 or .gz).
Agilent from 44 to 400K are supported.

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readAgilent(filePath, sampleName = NA,
    labName = NA, supFlags = TRUE, genome = c("hg19", "hg18", "hg38"),
    ploidy = 2, verbose = TRUE)

`filePath`	: string. A path to an Agilent FE (.txt) file.
`sampleName`	: string. A sample Id. Optional.
`labName`	: string. A lab Id. Optional.
`supFlags`	: should the flagged probes be suppressed. Default is `TRUE`.
`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. if `TRUE` (default), progress is printed.

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.

An object of class "rCGH"

Frederic Commo

readAffyCytoScan, readAffySNP6, readGeneric, readAffyOncoScan, setInfo, getInfo

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filePath <- system.file("extdata", "Agilent4x180K.txt.bz2", package = "rCGH")
cgh <- readAgilent(filePath, sampleName = "Agilent4x180K", labName = "myLab")
cgh