compute_supercells_DEA: Computes differential expression analysis for super-cells

In mariiabilous/SuperCellBM:

Description

Computes differential expression analysis for super-cells

Usage

compute_supercells_DEA(
  SC.list,
  SC.GE.list,
  cluster.name,
  ident.1 = NULL,
  ident.2 = NULL,
  seed = 12345,
  verbose = FALSE,
  pval.thresh = 0.05,
  logFC.thresh = 0,
  DO_unweighted = FALSE,
  ...
)

Arguments

SC.list	list of super-cells and other simplifications (output of compute_supercell)
SC.GE.list	list of super-cell gene expressions
cluster.name	name of clusterig result field
ident.1	name(s) of cluster for which markers are computed, if NULL (default), markers for all clusters will be computed (running supercell_FindAllMarkers instead of supercell_FindMarkers
ident.2	name(s) of clusters for comparison. If NULL (defauld), then all the other clusters used
seed	sandom seed to compute logFC_AUC score
DO_unweighted	whether to compute not sample-weighed DEA
...	other parameters of supercell_FindMarkers or supercell_FindAllMarkers

Value

list of DEA results for each super-cell like structure

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