ENCLfunc: Summarize single-cell ATAC-seq data according to ENCODE...

In WeiqiangZhou/SINTER: Single-cell genomic data integration

Description

This function is used for summarizing scATAC-seq data according to ENCODE clusters.

Usage

ENCLfunc(path, gr_ENCL, type = "paired")

Arguments

path	Directory to bam files of scATAC-seq data
gr_ENCL	GRanges object for ENCODE clusters
type	Sequencing read type. "paired" or "single" end read.

Value

data	Log2-transformed summarized data matrix.
lib	Total read counts (i.e., library size) for each single cell.

Examples

## Not run: 
scATAC_data <- ENCLfunc("/bam_file_path",gr_ENCL,type="paired")

## End(Not run)

WeiqiangZhou/SINTER documentation built on Sept. 11, 2019, 8:03 a.m.