normalise

normalise,ChIPprofile,character,numeric-method

normalise,ChIPprofile-method

normalise.ChIPprofile

object

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.

method

A numeric vector used to scale columns or rows.

normFactors


Various normalisation methods for ChIPprofile objects


The soGGi package provides a toolset to create genomic
interval aggregate/summary plots of signal or motif occurence
from BAM and bigWig files as well as PWM, rlelist, GRanges and
GAlignments Bioconductor objects. soGGi allows for
normalisation, transformation and arithmetic operation on and
between summary plot objects as well as grouping and subsetting
of plots by GRanges objects and user supplied metadata. Plots
are created using the GGplot2 libary to allow user defined
manipulation of the returned plot object. Coupled together,
soGGi features a broad set of methods to visualise genomics
data in the context of groups of genomic intervals such as
genes, superenhancers and transcription factor binding events.

Tom Carroll

soGGi

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

normalise function

Various normalisation methods for ChIPprofile objects

normalise: Normalise ChIPprofiles

Description

Usage

Arguments

Value

Examples