vulcan.annotate: Function to annotate peaks for VULCAN analysis

In vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Description

This function coalesces and annotates a set of BAM files into peak-centered data. It implements the ChIPPeakANno methods, with specific choices dealing with defining the genomic area around the promoter and which peaks to include.

Usage

vulcan.annotate(vobj, lborder = -10000, rborder = 10000,
  method = c("closest", "strongest", "sum", "topvar", "farthest",
  "lowvar"), TxDb = NULL)

Arguments

vobj	A list of peakcounts, samples and peakrpkms (i.e. the output of the function vulcan.import)
lborder	Boundary for peak annotation (in nucleotides) upstream of the Transcription starting site (default: -10000)
rborder	Boundary for peak annotation (in nucleotides) downstream of the Transcription starting site (default: 10000)
method	Method to deal with multiple peaks found within gene promoter boundaries. One of sum (default), closest, strongest, topvar, farthest or lowvar. This will affect only genes with multiple possible peaks. When a single peak can be mapped to the promoter region of the gene, that peak abundance will be considered as the gene promoter's occupancy. sum when multiple peaks are found, sum their contributions closest when multiple peaks are found, keep only the closest to the TSS as the representative one strongest when multiple peaks are found, keep the strongest as the representative one farthest when multiple peaks are found, keep only the closest to the TSS as the representative one topvar when multiple peaks are found, keep the most varying as the representative one lowvar when multiple peaks are found, keep the least varying as the representative one
TxDb	TxDb annotation object containing the knownGene track. If NULL (the default), TxDb.Hsapiens.UCSC.hg19.knownGene is loaded

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

samples

A vector of sample names and conditions

Examples

library(vulcandata)
vobj<-vulcandata::vulcanexample()
vobj<-vulcan.annotate(vobj,lborder=-10000,rborder=10000,method='sum')

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