Normalise ChIPprofiles

Share:

Description

Various normalisation methods for ChIPprofile objects

Usage

1
2
3
4
5
6
## S4 method for signature 'ChIPprofile'
normalise(object)

## S4 method for signature 'ChIPprofile,character,numeric'
normalise(object = "ChIPprofile",
  method = "rpm", normFactors = NULL)

Arguments

object

A ChIPprofile object

method

A character vector specifying normalisation method. Currently "rpm" for normalising signal for BAM to total reads, "quantile" to quantile normalise across samples, "signalInRegion" to normalise to proportion of signal within intervals, "normaliseSample" to normalise across samples and "normaliseRegions" to apply a normalisation across intervals.

normFactors

A numeric vector used to scale columns or rows.

Value

A ChIPprofile object

Author(s)

Thomas Carroll

Examples

1
2
data(chipExampleBig)
normalise(chipExampleBig,method="quantile",normFactors=1)