CountAPAc: Create a APA_cluster-Cell_Barcode count matrix for Seurart...

In HHengUG/hatpal2: APA clusters calling and analysis

Description

Create a APA_cluster-Cell_Barcode count matrix for Seurart analysis

Usage

CountAPAc(
  cluster_p,
  cluster_n,
  in_bamfile,
  cb_file,
  chr_info,
  out_dir,
  filter_method = "end",
  UBtag = "UB"
)

Arguments

cluster_p	Annotated APA clusters file of the positive strand, generated by AnnoAPAc()
cluster_n	Annotated APA clusters file of the positive strand, generated by AnnoAPAc()
in_bamfile	A indexed BAM file, and the index files (.bai) must be in the same directory of the indexed BAM
cb_file	A cell barcodes list, can be generated by extractAPA() or cellranger
chr_info	A data.table that contains the chrinfo, can be generated by ExtractChrinfo()
out_dir	The directory where a directory named "matrix/" is created and the output files are stored
filter_method	The way to filter reads (defult "end")
UBtag	UB tag (defult "UB")

Value

NULL. writes output in the directory "matrix/" of the out_dir

Examples

CountAPAc("p/APA_map.out.anno", "n/APA_map.out.anno", "test.bam", "_CBlist.txt", ExtractChrinfo("test.s.bam"), "output/")

HHengUG/hatpal2 documentation built on Dec. 17, 2021, 10:26 p.m.