Package 'vulcandata'

Title: VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset
Description: This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package.
Authors: Federico M. Giorgi [aut, cre], Andrew N. Holding [aut], Florian Markowetz [aut]
Maintainer: Federico M. Giorgi <[email protected]>
License: LGPL-3
Version: 1.35.1
Built: 2026-10-10 10:38:07 UTC
Source: https://github.com/bioc/vulcandata

Help Index

Function to load an example VULCAN dataset into the workspace

Description

This function loads a dummy ChIP-Seq dataset used for VULCAN examples.

Usage

vulcanexample()

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

vobj<-vulcanexample()
names(vobj)
vobj$peakcounts[1:5,]

Function to generate an import sheet CSV file for the vulcan test set

Description

This function generates a user-specific example sheet with appropriate paths on a dummy ChIP-Seq dataset

Usage

vulcansheet(outfile = "sheetfile.csv")

Arguments

outfile

Path and file name for the CSV sheet file

Value

nothing

Examples

vfile<-tempfile()
vulcansheet(vfile)
tmp<-read.csv(vfile)
head(tmp)
unlink(vfile)