ATAC objects — ATAC-class • mcATAC

ATAC is a shallow object holding ATAC data over cells/metacells. Minimally it needs to have an id, a description and a genome id.
ATACPeaks classes hold the data in the format of peaks and are used mostly for "trans" analysis.
ATACCounts classes hold the raw data in the format of sparse matrices - it can then be transformed into misha tracks.
ATACTracks classes hold pointers to tracks that hold the data at higher resolution (e.g. 20 bp), and can be used for "cis" analysis.

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)"
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 McATAC, or 'cell_id' and per-cell annotations for ScATAC. 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)
rna_egc: normalized gene expression per gene per metacell (optional). Can be created using add_mc_rna
order: order of the cells/metacells in the data (optional).