Detect_single_marker: Detect single markers of specific cell groups

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

Detect single markers of specific cell groups

Description

Detect single markers of specific cell groups

Usage

Detect_single_marker(
  scrna,
  id,
  step = 0.1,
  slot = "data",
  category = 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 = "human",
  self.db = NULL,
  self.db.only = F,
  ...
)

Arguments

scrna	seurat obj to be used
id	interested cell group
step	quantile steps
slot	indicate the slot of data to compute
category	Denotes which experiment 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)
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
self.db	self defined antibody database
self.db.only	Bolean. Only use the self deifned antibody database or not

Value

list of markers performance

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