binarise_files {Melissa} | R Documentation |
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.
binarise_files(indir, outdir = NULL, format = 1, no_cores = NULL)
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. |
No value is returned, the binarised data are stored in the outdir.
C.A.Kapourani C.A.Kapourani@ed.ac.uk
create_melissa_data_obj
, melissa
,
filter_regions
## Not run: # Met directory met_dir <- "name_of_met_dir" binarise_files(met_dir) ## End(Not run)