vulcan.import: Function to import BAM files
In federicogiorgi/vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Description Usage Arguments Value Examples

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

1	vulcan.import(sheetfile, intervals = NULL)

`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

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

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)