readAgilent {rCGH} | R Documentation

## 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"),
        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

[Package rCGH version 1.8.1 Index]