.Binarize {segmenter} | R Documentation

## Call Java `BinarizeBed`

### Description

Call the Java module `BinarizeBed` which binarize a bed file of the aligned reads.

### Usage

    .Binarize(inputdir, cellmarkfiletable, chromsizefile, binsize, outputdir, type)

### Arguments

`inputdir` | A string. The path to bed files.
`cellmarkfiletable` | A tab delimited files of three columns. The columns contains the cell, mark and the name or the bed file.
`chromsizefile` | A string. The path to the chromosomes sizes file.
`binsize` | An integer. The bin size to use. Default is 200.
`outputdir` | A string. The path to a directory where output will be written.
`type` | A string. The file type 'bam' or 'bed'.

### Value

`NULL`. Output files are written to the output directory.

### See Also

binarize_bed

[Package segmenter version 1.0.0 Index]