ScPeaks is a shallow object holding ATAC data over cells.
Minimally it should include a count matrix of peaks over cells, and PeakIntervals
which hold the coordinates
of the peaks.
Usage
# S4 method for ScPeaks
initialize(
.Object,
mat,
peaks,
genome,
id = NULL,
description = NULL,
metadata = NULL,
path = "",
tad_based = TRUE,
order = NULL
)
Arguments
- mat
a numeric matrix where rows are peaks and columns are cells. 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"
- 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)"
- metadata
data frame with a column called 'cell_id' and additional per-cell annotations, or the name of a delimited file which contains such annotations.
- path
path from which the object was loaded (optional)
- tad_based
wether the peak names are TAD-based
- order
order of the cells. If not provided, the order of the cells in the matrix is used.