runMagic

Input matrix c("bmat", "pmat", "gmat", "mmat").

input.mat

Number of steps for diffusion [3].

step.size

This function takes a snap object as input with bmat/pmat/gmat/mmat slot 
and run magic - an affinity graph-based method - to smooth the signal.

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.

runMagic: Affinity Graph-based Smoothing

Description

Usage

Arguments