vulcan.import: Function to import BAM files

In vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Description

This function coalesces and annotates a set of BAM files into peak-centered data

Usage

vulcan.import(sheetfile, intervals = NULL)

Arguments

sheetfile	path to a csv annotation file containing sample information and BAM location
intervals	size of the peaks. If NULL (default) it is inferred from the average fragment length observed in the dataset

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

samples

A vector of sample names and conditions

Examples

library(vulcandata)
# Generate an annotation file from the dummy ChIP-Seq dataset
vfile<-tempfile()
vulcandata::vulcansheet(vfile)
# Import BAM and BED information into a list object
# vobj<-vulcan.import(vfile)
# This vobj is identical to the object returned by
# vulcandata::vulcanexample()
unlink(vfile)

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