vulcan.normalize: Function to normalize promoter peak data
In vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Description Usage Arguments Value Examples

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

1	vulcan.normalize(vobj)

vobj

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

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

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

## End(Not run)