bin_counts | R Documentation |
Make bin count files from SAM files
bin_counts(SAM_dir, data_dir, cell_name, Nk = "5k")
SAM_dir |
The directory that contains the sorted SAM files with duplicates removed. The SAM file names: cellname.rmdup.sam. e.g. CJA1023.rmdup.sam The bin count files will also be saved in SAM_dir. The output bin count file names: cellname.varbin.Nk.txt, cellname.varbin.Nk.stats.txt e.g. CJA1023.varbin.20k.txt, CJA1023.varbin.20k.stats.txt |
data_dir |
The directory that contains the bin boundary file; also contains mappable region files such as chrom.mappable.txt, mappable.regions.sorted.txt, chrom.sizes.txt |
cell_name |
The cell name. |
Nk |
Default value: 5k. It denotes the number of bins. 5000 = 5k, 10000 = 10k, ... |
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