runHarmony

A vector of the components to use in construction of the KNN graph.

eigs.dim

Either (1) Dataframe with variables to integrate or (2) vector with labels.

meta_data

If meta_data is dataframe, this defined which variable(s) to remove (character vector).

vars_use

Integration of single cell ATAC-seq data for batch correction using Harmony algorithm

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.

runHarmony: Perform batch effect using harmony

Description

Usage

Arguments