rCGH (version 1.2.2)

readAgilent: Agilent Dual-Color Hybridization "rCGH-Agilent" Constructor.

Description

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.

Usage

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

Arguments

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.

verbose

: logical. if 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.

See Also

readAffyCytoScan, readAffySNP6, readGeneric, setInfo, getInfo

Examples

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