binarize_bam {segmenter} | R Documentation |
Transform the aligned reads into a binary format.
binarize_bam( inputdir, cellmarkfiletable, chromsizefile, binsize = 200, outputdir )
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. |
NULL. Write files to the outputdir
Binarize binarize_bed
# 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')