Identify potential marker genes for each cluster.
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
)scCATCH object
scCATCH object generated from createscCATCH.
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.
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.
Whether to use custom markers data.frame.
A data.frame containing marker genes. See demo_marker. Default is to use the system cellmatch data.frame.
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 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.
'1' is to compare with other every cluster. '2' is to compare with other clusters together.
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.
Include the gene detected in at least this many cells in each cluster.
Include the gene with at least this fold change of average gene expression compared to every other clusters.
Include the significantly highly expressed gene with this cutoff of p value from wilcox test compared to every other clusters.
Show progress messages.
Details of available tissues see https://github.com/ZJUFanLab/scCATCH/wiki