Detect single markers of all cell groups

Source: R/Cell_markers.ident.R

Detect single markers of all cell groups

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