process.hmc: Processing hmC information from the MLML output
Description
Processing MLML software output to generate files with hmC and CpG methylation information.
Usage
process.hmc(file, output_folder, Coverage)
Arguments
file
character; the path to the file
output_folder
character; the path to the output files
Coverage
GRanges; the object containing coverage for each cytosine
Value
The function will return two files one each for "CpG" and "hmC" for the given sample which can directly be used for BSdata object creation.
Details
This function allows processing of the output files from MLML software (Qu et al, Bioinformatics 2013).
MLML read counts from BS-seq, oxBS-seq and TAB-seq to provide simultaneous estimates of 5hmC and 5mC levels. The
input for this function is output file from this software alongwith a GRanges object consisting of coverage
of each cytosine. The GRanges object should contain "coverage" column. This object can be generated using the
coverage method of R package GenomicRanges.