vulcan.normalize: Function to normalize promoter peak data

Description Usage Arguments Value Examples

View source: R/vulcan.R

Description

This function normalizes gene-centered ChIP-Seq data using VST

Usage

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Arguments

vobj

a list, the output of the 'vulcan.annotate' function

Value

A list of components:

peakcounts

A matrix of raw peak counts, peaks as rows, samples as columns

peakrpkms

A matrix of peak RPKMs, peaks as rows, samples as columns

rawcounts

A matrix of raw gene counts, genes as rows, samples as columns. The counts are associated to the promoter region of the gene

rpkms

A matrix of RPKMs, genes as rows, samples as columns. The RPKMs are associated to the promoter region of the gene

normalized

A matrix of gene abundances normalized by Variance-Stabilizing Transformation (VST), genes as rows, samples as columns. The abundances are associated to the promoter region of the gene

samples

A vector of sample names and conditions

Examples

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## Not run: 
library(vulcandata)
vobj<-vulcandata::vulcanexample()
vobj<-vulcan.annotate(vobj,lborder=-10000,rborder=10000,method='sum')
vobj<-vulcan.normalize(vobj)

## End(Not run)

vulcan documentation built on Nov. 8, 2020, 8:15 p.m.