make_metacells: Make metacells

View source: R/make_metacells.R

make_metacellsR Documentation

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 May 3, 2022, 4:34 a.m.