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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.