Set use_method 1 to compare with every other cluster. Besides, users can set comp_cluster, it represent the 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.
# The most strict condition to identify marker genes
obj <- findmarkergene(object = obj, species = "Mouse", marker = cellmatch,tissue = "Kidney", use_method = "1")
# Other conditions to identify marker genes
obj <- findmarkergene(object = obj,species = "Mouse", marker = cellmatch, tissue = "Kidney", use_method = "1", comp_cluster = 1)
Set use_method 2 to compare with other clusters together like the strategy in Seurat
# The most loose condition to identify marker genes
obj <- findmarkergene(object = obj, species = "Mouse", marker = cellmatch, tissue = "Kidney", use_method = "2")
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