binarize_bam {segmenter}R Documentation

Binarize the bam files

Description

Transform the aligned reads into a binary format.

Usage

binarize_bam(
  inputdir,
  cellmarkfiletable,
  chromsizefile,
  binsize = 200,
  outputdir
)

Arguments

inputdir

A string. The dirctory of the bam files.

cellmarkfiletable

A string. The path to the input files table. Only

chromsizefile

A string. The path to the chromosomes sizes file.

binsize

An integer. The number in bp used to generate binarized files.

outputdir

A string. The path to a directory where output will be written.

Value

NULL. Write files to the outputdir

See Also

Binarize binarize_bed

Examples

# locate input and output files
inputdir <- system.file("extdata", package = "bamsignals")
cellmarkfiletable <- system.file('extdata',
                                 'cell_mark_table.tsv',
                                 package = 'segmenter')
chromsizefile <- system.file('extdata/CHROMSIZES',
                             'hg18.txt',
                              package = 'chromhmmData')
outputdir <- tempdir()

# run command
binarize_bam(inputdir,
             chromsizefile = chromsizefile,
             cellmarkfiletable = cellmarkfiletable,
             outputdir = outputdir)

# show output files
list.files(outputdir, pattern = '*_binary.txt')


[Package segmenter version 0.99.14 Index]