satacprocess: Preprocess scATAC-seq

In Winnie09/SCATE: SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

Preprocess scATAC-seq

Description

Preprocessing scATAC-seq samples

Usage

satacprocess(input, type = "bam", libsizefilter = 1000)

Arguments

input	Either a character vector of locations to bam files (when type is bam) or list of GRanges object of scATAC-seq reads (when type is gr).
type	Either 'bam' or 'gr'. 'bam' if the input is locations to bam files. 'gr' if the input is a list of GRanges object.
libsizefilter	Numeric variable giving the minimum library size. scATAC-seq samples with library size smaller than this cutoff will be discarded.

Details

This function filters out scATAC-seq with low library size and transforms the reads into middle points of the reads.

Value

GRanges object of list of GRanges object after preprocessing.

Author(s)

Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji* <[e-mail]>

Examples

c1 <- GRanges(seqnames="chr1",IRanges(start=seq_len(100)+1e6,end=seq_len(100)+1e6))
c2 <- GRanges(seqnames="chr2",IRanges(start=seq_len(100)+1e6,end=seq_len(100)+1e6))
grl <- list(cell1=c1,cell2=c2)
satacprocess(grl,type='gr',libsizefilter=10)

Winnie09/SCATE documentation built on May 10, 2023, 8:10 a.m.