vulcan.import {vulcan} | R Documentation |
This function coalesces and annotates a set of BAM files into peak-centered data
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:
A matrix of raw peak counts, peaks as rows, samples as columns
A matrix of peak RPKMs, peaks as rows, samples as columns
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)