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

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

View source: R/buildData.R

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

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

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.

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

See Also

readAffyCytoScan, readAffySNP6, readGeneric, readAffyOncoScan, setInfo, getInfo

Examples

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

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