binarise_files: Binarise CpG sites

In andreaskapou/Melissa: Bayesian clustering and imputationa of single cell methylomes

Description

Script for binarising CpG sites and formatting the coverage file so it can be directly used from the BPRMeth package. The format of each file is the following: <chr> <start> <met_level>, where met_level can be either 0 or 1. To read compressed files, e.g ending in .gz or .bz2, the R.utils package needs to be installed.

Usage

binarise_files(indir, outdir = NULL, format = 1, no_cores = NULL)

Arguments

indir	Directory containing the coverage files, output from Bismark.
outdir	Directory to store the output files for each cell with exactly the same name. If NULL, then a directory called 'binarised' inside 'indir' will be create by default.
format	Integer, denoting the format of coverage file. When set to '1', the coverage file format is assumed to be: "<chr> <start> <end> <met_prcg> <met_reads> <unmet_reads>". When set to '2', then the format is assumed to be: "<chr> <start> <met_prcg> <met_reads> <unmet_reads>".
no_cores	Number of cores to use for parallel processing. If NULL, no parallel processing is used.

Value

No value is returned, the binarised data are stored in the outdir.

Author(s)

C.A.Kapourani [e-mail]

See Also

create_melissa_data_obj, melissa, filter_regions

Examples

## Not run: 
# Met directory
met_dir <- "name_of_met_dir"

binarise_files(met_dir)

## End(Not run)

andreaskapou/Melissa documentation built on June 12, 2020, 5:54 p.m.