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

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

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"),
    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

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

fredcommo/rCGH documentation built on May 16, 2019, 2:41 p.m.