findmarkergene: Find potential marker genes for each cluster

In scCATCH: Single Cell Cluster-Based Annotation Toolkit for Cellular Heterogeneity

Find potential marker genes for each cluster

Description

Identify potential marker genes for each cluster.

Usage

findmarkergene(
  object,
  species = NULL,
  cluster = "All",
  if_use_custom_marker = FALSE,
  marker = NULL,
  cancer = "Normal",
  tissue = NULL,
  use_method = "1",
  comp_cluster = NULL,
  cell_min_pct = 0.25,
  logfc = 0.25,
  pvalue = 0.05,
  verbose = TRUE
)

Arguments

object	scCATCH object generated from createscCATCH.
species	The specie of cells. The species must be defined. 'Human' or 'Mouse'. When if_use_custom_marker is set TRUE, no need to define the species.
cluster	Select which clusters for potential marker genes identification. e.g. '1', '2', etc. The default is 'All' to find potential makrer genes for each cluster.
if_use_custom_marker	Whether to use custom markers data.frame.
marker	A data.frame containing marker genes. See demo_marker. Default is to use the system cellmatch data.frame.
cancer	If the sample is from cancer tissue, then the cancer type may be defined. When if_use_custom_marker is set TRUE, no need to define the cancer.
tissue	Tissue origin of cells must be defined. Select one or more related tissue types. When if_use_custom_marker is set TRUE, no need to define the tissue.
use_method	'1' is to compare with other every cluster. '2' is to compare with other clusters together.
comp_cluster	Number of clusters to compare. Default is to compare all other cluster for each cluster. Set it between 1 and length of unique clusters. More marker genes will be obtained for smaller comp_cluster.
cell_min_pct	Include the gene detected in at least this many cells in each cluster.
logfc	Include the gene with at least this fold change of average gene expression compared to every other clusters.
pvalue	Include the significantly highly expressed gene with this cutoff of p value from wilcox test compared to every other clusters.
verbose	Show progress messages.

Details

Details of available tissues see https://github.com/ZJUFanLab/scCATCH/wiki

Value

scCATCH object

scCATCH documentation built on April 23, 2023, 5:09 p.m.