normalise: Normalise ChIPprofiles

In soGGi: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

Description

Various normalisation methods for ChIPprofile objects

Usage

## 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

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

soGGi documentation built on Nov. 8, 2020, 5:24 p.m.