make_metacells: Make metacells

In jmonlong/scCNAutils: Functions to analyze copy number aberrations in single-cell data

Make metacells

Description

Randomly select cells in each community and merge them to create metacells with higher resolution.

Usage

make_metacells(
  ge_df,
  comm_df,
  nb_metacells = 10,
  metacell_size = 3,
  baseline_cells = NULL,
  nb_cores = 1,
  max_baseline_comm = 3
)

Arguments

ge_df	gene expression of all cells
comm_df	a data.frame with community information, output from find_communities.
nb_metacells	the number of metacells per comunity.
metacell_size	the number of cells in a metacell.
baseline_cells	the cells to use for baseline communities.
nb_cores	the number of processor to use.
max_baseline_comm	the maximum number of baseline communities to generate.

Value

a list with

ge	a data.frame with coordinates and gene expression for each metacell.
info	information about which metacell correspond to which community.
mc_cells	information about which cells were used for each metacell.

Author(s)

Jean Monlong

jmonlong/scCNAutils documentation built on Feb. 8, 2025, 8:09 a.m.