process.hmc: Processing hmC information from the MLML output

In methylPipe: Base resolution DNA methylation data analysis

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)

methylPipe documentation built on Nov. 8, 2020, 6:51 p.m.