vulcan.annotate: Function to annotate peaks for VULCAN analysis

Description Usage Arguments Value Examples

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

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

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

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

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

federicogiorgi/vulcan documentation built on May 27, 2019, 7:25 a.m.