identifyMarkers: Identify marker genes associated with cell clusters

In amsszlh/scMC: Integrating and comparing multiple single cell genomic datasets

Description

Identify marker genes associated with cell clusters

Usage

identifyMarkers(
  object,
  mode = c("separate", "integrated"),
  features = NULL,
  test.use = "wilcox",
  only.pos = TRUE,
  min.pct = 0.25,
  logfc.threshold = 0.25,
  ...
)

Arguments

object	a lsit of Seurat objects or a single Seurat object
mode	"separate" or "integrated"; "separate" means identifying marker genes of cell clusters from each dataset separately, and "integrated" means identifying marker genes of cell clusters from the integrated data
features	features used to perform statistical test
test.use	which test to use
only.pos	Only return positive markers
min.pct	Threshold of the percent of cells enriched in one cluster
logfc.threshold	Threshold of Log Fold Change
...	other parameters in FindAllMarkers

amsszlh/scMC documentation built on Jan. 2, 2021, 1:51 p.m.