Detect single markers of specific cell groups

Source: R/Cell_markers.ident.R

Detect single markers of specific cell groups

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