vulcan.normalize {vulcan} | R Documentation |
This function normalizes gene-centered ChIP-Seq data using VST
vulcan.normalize(vobj)
vobj |
a list, the output of the |
A list of components:
A matrix of raw peak counts, peaks as rows, samples as columns
A matrix of peak RPKMs, peaks as rows, samples as columns
A matrix of raw gene counts, genes as rows, samples as columns. The counts are associated to the promoter region of the gene
A matrix of RPKMs, genes as rows, samples as columns. The RPKMs are associated to the promoter region of the gene
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
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)