SuperCell (version 1.0)

supercell_FindAllMarkers: Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindAllMarkers (for simplicity)

Description

Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindAllMarkers (for simplicity)

Usage

supercell_FindAllMarkers(
  ge,
  clusters,
  supercell_size = NULL,
  genes.use = NULL,
  logfc.threshold = 0.25,
  min.expr = 0,
  min.pct = 0.1,
  seed = 12345,
  only.pos = FALSE,
  return.extra.info = FALSE,
  do.bootstrapping = FALSE
)

Value

list of results of supercell_FindMarkers

Arguments

ge

gene expression matrix for super-cells (rows - genes, cols - super-cells)

clusters

a vector with clustering information (ordered the same way as in ge)

supercell_size

a vector with supercell size (ordered the same way as in ge)

genes.use

set of genes to test. Defeult -- all genes in ge

logfc.threshold

log fold change threshold for genes to be considered in the further analysis

min.expr

minimal expression (default 0)

min.pct

remove genes with lower percentage of detection from the set of genes which will be tested

seed

random seed to use

only.pos

whether to compute only positive (upregulated) markers

return.extra.info

whether to return extra information about test and its statistics. Default is FALSE.

do.bootstrapping

whether to perform bootstrapping when computing standard error and p-value in wtd.t.test