process.hmc {methylPipe} | R Documentation

## 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

### 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.

### 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.

### Author(s)

Kamal Kishore

### See Also

`BSdata-class`

### Examples

    #process.hmc(file,"/path-to-output/", Coverage)

[Package methylPipe version 1.20.0 Index]