readGeneric {rCGH} | R Documentation

## Generic rCGH object `"rCGH-generic"` Constructor

### Description

A constructor function which takes a tabulated .txt file as input, possibly in a compressed format (.bz2 or .gz). Notice that precise column names are mandatory, see the `details` section.

### Usage

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

### Arguments

`filePath` | : string. A path to an Generic .txt file.
`sampleName` | : string. A sample Id. Optional.
`labName` | : string. A lab Id. Optional.
`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. When `TRUE` (default), progress is printed.

### Details

This generic constructor does not expect any preamble. Mandatory columns are:

`ProbeName`:

  Character strings. Typicaly the probe ids.

`ChrNum`:

  numeric. The chromosome numbers. In case Chr X and Y are used and named as `"X"` and `"Y"`, these notations will be converted into 23 and 24, respectively.

`ChrStart`:

  numeric. The chromosomal probes locations.

`Log2Ratio`:

  numeric. The corresponding Log2Ratios.

### Value

An object of class `"rCGH"`

### Author(s)

Frederic Commo

### See Also

`readAgilent`, `readAffySNP6`, `readAffyCytoScan`, `readAffyOncoScan`, `setInfo`, `getInfo`

### Examples

    filePath <- system.file("extdata", "generic.txt.bz2", package = "rCGH")
    cgh <- readGeneric(filePath, sampleName = "demo")
    cgh

[Package rCGH version 1.16.0 Index]