Detect_single_marker_all: Detect single markers of all cell groups

In CostaLab/sc2marker: Detect marker panel from scRNA-seq profile

Detect single markers of all cell groups

Description

Detect single markers of all cell groups

Usage

Detect_single_marker_all(
  scrna,
  step = 0.1,
  slot = "data",
  category = NULL,
  clusters_to_detect = NULL,
  geneset = NULL,
  assay = "RNA",
  do.fast = F,
  min.pct = 0.15,
  min.fc = 0.25,
  use.all = F,
  do.f1score = F,
  pseudo.count = 0.01,
  min.tnr = 0.65,
  org = "mouse",
  self.db = NULL,
  self.db.only = F,
  ...
)

Arguments

scrna	seurat obj to be used
step	quantile steps
slot	indicate the slot of data to compute
clusters_to_detect	set of clusters for compupation
geneset	custom genes to test
assay	indicate the assay to compute
min.pct	only test genes that are detected in a minimum fraction of cells in interested cell types. Default is 0.15
use.all	Don't do any filter on input geneset
org	Choose database for human or mouse
self.db	self defined antibody database
self.db.only	Bolean. Only use the self deifned antibody database or not
id	interested cell group
test.use	Denotes which test to use. Available options are: "IHC" : use genes with valid antibody for IHC in human protein atlas "ICC" : use genes with valid antibody for ICC in human protein atlas "ICC.IHC" : use genes with valid antibody for ICC or IHC in human protein atlas "Flow" : Only use cell surface genes with at least one valid antibody(ICC or IHC)

Value

list of markers performance

CostaLab/sc2marker documentation built on May 12, 2022, 6:05 a.m.