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 1.28.0 Index]