ATACPeaks objects — ATACPeaks-class • mcATAC

ATACPeaks is a shallow object holding ATAC data over cells/metacells. Minimally it should include a count matrix of peaks over cells/metacells, PeakIntervals which hold the coordinates of the peaks and the id of the genome assembly of the peaks. ScPeaks and McPeaks extend the ATACPeaks object by adding metadata and additional slots.

Slots

id: an identifier for the object, e.g. "pbmc".
description: description of the object, e.g. "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)"
mat: a numeric matrix where rows are peaks and columns are cells/metacells. Can be a sparse matrix.
peaks: misha intervals set. Can contain a field named 'peak_name' with a unique name per peak. Both the names and intervals should be unique (a peak cannot appear more than once).
genome: genome assembly of the peaks. e.g. "hg38", "hg19", "mm9", "mm10"
metadata: data frame with a column called 'metacell' and additional metacell annotations for McPeaks, or 'cell_id' and per-cell annotations for ScPeaks. The constructor can also include or the name of a delimited file which contains such annotations.
path: original path from which the object was loaded (optional)
promoters: are the peaks promoters (optional). When peaks are promoters the peak name would be the gene name instead of coordinates.
tad_based: are the peaks named based on TADs.