compute_supercells_metacells_with_min_mc_size: compute super-cell like structure of metacells (based on...

In mariiabilous/SuperCellBM:

Description

compute super-cell like structure of metacells (based on provided 'min_mc_size' instead of 'min_mc_size' as min supercell size)

Usage

compute_supercells_metacells_with_min_mc_size(
  sc.counts,
  min_mc_size_seq,
  proj.name,
  ToComputeSC,
  genes.use = NULL,
  SC.list = NULL,
  mc.k.knn = 100,
  T_vm_def = 0.08,
  MC.folder = "MC",
  MC_gene_settings = c("Metacell_default", "Metacell_SC_like"),
  verbose = FALSE
)

Arguments

sc.counts	single-cell count matrix (genes by cells)
min_mc_size_seq	vector of min metacell sizes (to varry graining levels)
proj.name	project name to initiame MC and store MC outputs
ToComputeSC	if TRUE computes metacells, if FALSE, loads from corresponding folder
genes.use	genes used to build super-cells (for MC_gene_settings == 'Metacell_SC_like'), can be ommited if SC.list is provided
mc.k.knn	metacell k for knn
T_vm_def	metacell cutoff for variable genes
MC.folder	MC folder to store output
MC_gene_settings	do not touch :)

mariiabilous/SuperCellBM documentation built on Jan. 28, 2022, 7:45 p.m.