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Use markers from different species

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Shao, Xin edited this page Jan 8, 2023 · 1 revision

You can first create a custom_marker data.frame and then use it in findmarkergene()

e.g., scRNA-seq data from rat

custom_marker <- data.frame(species = c("Rat", "Rat", "Rat", "Rat"),
                            tissue = c("Liver", "Liver", "Liver", "Liver"),
                            cancer= c("Normal", "Normal", "Normal", "Normal"),
                            condition = c("Normal cell", "Normal cell", "Normal cell", "Normal cell"),
                            subtype1 = c("NA", "NA", "NA", "NA"),
                            subtype2 = c("NA", "NA", "NA", "NA"),
                            subtype3 = c("Periportal", "Periportal", "Pericentral", "Pericentral"),
                            celltype = c("Hepatocyte", "Hepatocyte", "Hepatocyte", "Hepatocyte"),
                            gene = c("Cyp2f2", "Alb", "Glul", "Cyp2e1"),
                            resource = c("Experiment", "Experiment", "Experiment", "Experiment"),
                            pmid = c("28166538", "28166538", "28166538", "28166538"), stringsAsFactors = FALSE)

obj <- findmarkergene(object = obj, species = "Rat", marker = custom_marker, tissue = "Liver")
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