makeGR {epihet} | R Documentation |
Creates a GenomicRanges object for each methclone output file
makeGR(files, ids, cores = 5, sve = FALSE)
files |
A vector of input files containing methclone output files, the suffix of files should be methClone_out.gz |
ids |
A vector of sample ids 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) |
A list, each element is a data frame of GenomicRanges objects containing pdr, epipolymorphism, and Shannon entropy values for each input file. Saves as an epi.gr.rda extension
path <- system.file('extdata', package = 'epihet') files <- dir(path = path, pattern = 'methClone_out.gz', recursive = TRUE, full.names = TRUE) ids <- basename(dirname(files)) GR.List <- epihet::makeGR(files = files, ids = ids, cores = 1, sve = FALSE)