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Given metacells (usually from RNA data), project ATAC counts to get a McPeaks object

Source: R/project_on_mc.R
project_atac_on_mc.Rd

Given cell to metacell association, summarise atac counts to generate a McPeaks object. project_atac_on_mc_from_metacell1 projects given a metacell1 'mc' object, while project_atac_on_mc_from_h5ad uses the output of the 'metacells' python package (metacell2).

Usage

project_atac_on_mc(
  atac,
  cell_to_metacell = NULL,
  metadata = NULL,
  min_int_frac = 0.5,
  mc_size_eps_q = 0.1,
  id = NULL,
  description = NULL,
  rm_zero_peaks = TRUE,
  ignore_metacells = c(-1, -2)
)

project_atac_on_mc_from_metacell1(
  atac,
  scdb,
  mc_id,
  metadata = NULL,
  id = NULL,
  description = NULL
)

project_atac_on_mc_from_h5ad(
  atac,
  h5ad_file,
  min_int_frac = 0.5,
  metadata = NULL,
  id = NULL,
  description = NULL
)

Arguments

atac

an ScPeaks object

cell_to_metacell

a data frame with a column named "cell_id" with cell id and another column named "metacell" with the metacell the cell is part of.

metadata

(optional) per-metacell metadata. A data frame with a column called 'metacell' and additional metacell annotations.

min_int_frac

(optional) minimal expected fraction of intersection of barcodes (cell names) in ScPeaks

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.

id

an identifier for the object, e.g. "pbmc". If NULL - the id would be taken from the scATAC object atac.

description

an identifier for the object, e.g. "pbmc". If NULL - the description would be taken from the scATAC object atac

rm_zero_peaks

remove peaks without any reads (all-zero peaks). Default: TRUE

ignore_metacells

a vector of metacells to ignore. Default: -1, -2 (the "outliers" metacell in the metacell2 python package).

scdb

a metacell1 scdb path

mc_id

id of the metacell object within scdb

h5ad_file

name of an h5ad file which is the output of 'metacells' python package.

Value

an McPeaks object

Examples

if (FALSE) {
atac_sc <- import_from_10x("pbmc_data", genome = "hg38")
data(cell_to_metacell_pbmc_example)
atac_mc <- project_atac_on_mc(atac_sc, cell_to_metacell_pbmc_example)
}