.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 0.99.14 Index]