bin_counts: make bin count files

In JunyanSong/SCclust: Single Cell Copy Number Analysis and Clustering

make bin count files

Description

Make bin count files from SAM files

Usage

bin_counts(SAM_dir, data_dir, cell_name, Nk = "5k")

Arguments

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, ...

JunyanSong/SCclust documentation built on April 16, 2022, 8:44 p.m.