cellmatch is the system data.frame containing the known markers of human and mouse.
demo_marker to build a new one.demo_marker()
#> species tissue cancer condition subtype1 subtype2
#> 1 Human Liver Normal Normal cell NA CD4+
#> 2 Human Liver Normal Normal cell NA CD8+
#> 3 Human Liver Hepatocellular Cancer Cancer cell NA NA
#> 4 Human Liver Hepatocellular Cancer Cancer cell Regulatory NA
#> subtype3 celltype gene resource pmid
#> 1 NA T Cell CD4 Experiment 27781378
#> 2 NA T Cell CD8A Experiment 27781378
#> 3 Exhausted T Cell ABCG1 Single-cell sequencing 28622514
#> 4 NA T Cell ACP5 Single-cell sequencing 28622514
custom_marker data.frame and then use it in findmarkergene()
custom_marker <- data.frame(species = c("Mouse", "Mouse", "Mouse", "Mouse"),
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 = "Mouse", marker = custom_marker, tissue = "Liver")
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