satacprocess: Preprocess scATAC-seq

Description Usage Arguments Details Value Author(s) Examples

View source: R/satacprocess.R

Description

Preprocessing scATAC-seq samples

Usage

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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* <whou10@jhu.edu>

Examples

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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)

SCATE documentation built on Nov. 8, 2020, 5:56 p.m.