makeGR: Make List of GenomicRanges Object

In xiaowenchenjax/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description

Creates a GenomicRanges object for each bisulfite sequencing data file

Usage

makeGR(files, ids, cores = 5, sve = FALSE)

Arguments

files	A vector of input files containing bisulfite sequencing data
ids	A vector of sample id's for the files
cores	The number of cores to be used for parallel execution (default: 5)
sve	A boolean to save the GenomicRanges object (default: FALSE)

Value

A data frame of GenomicRanges objects containing pdr, epipolymorphism, and Shannon entropy values for all input files. Saves as an epi.gr.rda extension

Examples

path = system.file('extdata', package = 'epihet')
files = dir(path = path, pattern = '\\.bam$',
            recursive = TRUE, full.names = TRUE)[c(1,2)]
ids = basename(dirname(files))[c(1,2)]
GR.List = epihet::makeGR(files = files, ids = ids,
cores = 1, sve = FALSE)

xiaowenchenjax/epihet documentation built on May 5, 2019, 9:20 a.m.