ATACTracks objects — ATACTracks-class • mcATAC

ATACTracks is a shallow object holding ATAC data over cells/metacells. Minimally it should include a vector of track names which hold the names of the tracks with the ATAC data. McTracks extend the ATACTracks object by adding metadata and additional slots.

Slots

tracks: vector of track names with the ATAC data.
total_cov: vector with total coverage of the tracks.
marginal_track: name of a track with marginal coverage.
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. The constructor can also include or the name of a delimited file which contains such annotations.
resolution: the resolution of the tracks.
window_size: The size of the window used to smooth the counts in each track. If no smoothing was done - this should be equal to resolution/2