createPmat

A GRanges object contains the peaks

peaks

A numeric class that indicates the number of cells to calculate per processing core [20].

ncell.chunk

A logical variable indicates if run this using multiple processors [TRUE].

do.par

num.cores

This function takes a snap object and peak list as input and creates cell-by-peak matrix

A fast and accurate analysis toolkit for single cell ATAC-seq. Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and reveal cell-type specific regulatory landscapes. However, the exceeding data sparsity has posed unique challenges for the data analysis. SnapATAC is an end-to-end bioinformatics pipeline for analyzing large-scale single cell ATAC-seq data which includes quality control, normalization, clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data. See Preissl S, Fang R, et al (2018) <doi:10.1038/s41593-018-0079-3> for more details.

createPmat: Create Cell-by-Peak Matrix

Description

Usage

Arguments

Value