Center single-cell ATAC-seq count data

Function to center raw read counts for scATAC-seq data based on mean reads in features/rows (e.g. peaks) per cell

Usage

centerCounts(obj, doInChunks = TRUE, chunkSize = 1000)

obj: Either a RangedSummarizedExperiment-class or dgeMatrix-class object of the single-cell ATAC data (peaks x cells) to center raw data for
doInChunks: boolean value whether or not to score cells in chunks (useful for large scATAC datasets of > 5,000 cells). If TRUE, cells are centered sequentially in chunks of size=1000 cells at a time to avoid memory limitations, and eventually merged (column-wise). Overriden and set to TRUE if > 10,000 cells in dataset
chunkSize: numeric specifying the number of cells to perform centering for at once, if running in chunks (to save memory). Default is 1000

Either a RangedSummarizedExperiment-class or dgeMatrix-class object with counts centered by mean reads in peaks per cell

Vinay Kartha