Create an ScPeaks,McPeaks object from matrix and peaks

Usage

import_from_matrix(
  mat,
  peaks,
  genome,
  id = NULL,
  description = NULL,
  metadata = NULL,
  class = "ScPeaks",
  rm_zero_peaks = TRUE,
  tad_based = TRUE,
  zero_based = FALSE,
  mc_size_eps_q = 0.1
)

Arguments

mat: a matrix/sparse matrix of counts
peaks: an intervals set where each row corresponds to a row in mat. Can contain an additional column named 'peak_name' with peak names, in which case the rownames of mat are expected to equal to this column.
genome: genome assembly of the peaks. e.g. "hg38", "hg19", "mm9", "mm10"
id: an identifier for the object, e.g. "pbmc". If NULL - a random id would be assigned.
description: (Optional) description of the object, e.g. "PBMC from a healthy donor - granulocytes removed through cell sorting (10k)".
metadata: (Optional) data frame with a column called 'metacell' and additional metacell annotations, or the name of a delimited file which contains such annotations.
class: should the output object be a ScPeaks or McPeaks
rm_zero_peaks: remove peaks without any reads (all-zero peaks). Default: TRUE
tad_based: whether to name peaks based on TADs if possible (when an intervals set named "intervs.global.tad_names" exists). When FALSE - peaks are named based on their coordinates.
zero_based: are the coordinates of the features 0-based? Note that when this is FALSE (default) the coordinates of the created object would be different from the ones in features_fn by 1 bp.
mc_size_eps_q: (optional) quantile of MC size (in UMIs) to scale the number of UMIs per metacell. \(egc_ij\) would then be the fraction of peak i in metacell j multiplied by the mc_size_eps_q quantile of metacell sizes.

Examples

if (FALSE) {
atac_sc <- import_from_matrix(mat, peaks, genome = "hg38")
atac_mc <- import_from_matrix(mat, peaks, genome = "hg38", class = "McPeaks")
}