gcNorm {CNAnorm} | R Documentation

## Methods for Function gcNorm in Package ‘CNAnorm’

### Description

`gcNorm` perform GC content normalization on ratio Test/Normal in Package ‘CNAnorm’

### Usage

    ## S4 method for signature 'CNAnorm'
    gcNorm(object, exclude = character(0), maxNumPoints = 10000)

### Arguments

`object` | An object of Class `"CNAnorm"`
`exclude` | A character vector with name of chromosomes/contigues not to use to calculate GC content correction. All genome, however, will be corrected
`maxNumPoints` | Maximum number of data points to fit the loess correction. For computational pourposes, if the number of points in `ratio(object)` is greater than `maxNumPoints`, only `maxNumPoints` randomly selected will be used

### Value

An object of class `"CNAnorm"`

### Methods

`signature(object = "CNAnorm")`

  Perform GC content correction on an object of class `"CNAnorm"`. Returns the same object with corrected ratio

### Author(s)

Stefano Berri <s.berri@leeds.ac.uk>

### See Also

`loess`, `CNAnorm-class`, `ratio`

### Examples

    data(LS041)
    CN <- dataFrame2object(LS041)
    # correct for GC content, but ignoring data from sex chromosomes and
    # mitocondria
    CN.gcNorm <- gcNorm(CN, exclude = c("chrX", "chrY", "chrM"))

[Package CNAnorm version 1.38.0 Index]