bedtoolsr: Counting reads mapped to a specified region using bedtools
In Liuy12/MBDDiff: MBDDiff for processing MBDcap-seq datasets

Description Usage Arguments Details Value Author(s) References Examples

Given bam file or directories of bam files, counting reads mapped to genomic intervals specified by user.

1	bedtoolsr(bam = NULL, bamdir = NULL, bed)

`bam`	bam file, including absolute path of the file. This is usually the output of alignment programs like, bwa, bowtie, etc.
`bamdir`	Alternatively, you can also provide the path of a list of bam files to process all at once.
`bed`	beb files, which include genomic intervels you want to measure.

This function is basically a wrapper for bedtools, which means you still need to have bedtools installed on your computer and saved in your system path.

A list of two elements:

`count`	a vector or matrix of values that indicates the number of reads that mapped to user-specified intervals
`gaplength`	a integer vector that indicates the gap length of user-specified intervals

Yuanhang Liu

https://github.com/Liuy12/MBDDiff

## Not run: 
	# Process several bam files in a fold 
	Promoter_counts <- bedtoolsr(bamdir = '/path/to/bam/files', bed = '/path/to/bed/file')
	
## End(Not run)