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Select different combination of tissues or cancers for annotation

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

[1] Use parameters of tissue and cancer in findmarkergene()

e.g., scRNA-data from human blood samples:

obj <- findmarkergene(object = obj,
                      species = "Human",
                      marker = cellmatch,
                      tissue = c("Blood", "Peripheral blood", "Plasma", "Serum", "Umbilical cord blood"))

e.g., scRNA-data from human colon samples:

obj <- findmarkergene(object = obj,
                      species = "Human",
                      marker = cellmatch,
                      tissue = c("Blood", "Peripheral blood", "Serum", "Colon", "Colorectum", "Intestine")),
                      cancer = c("Colon Cancer", "Colorectal Cancer"))

[2] Use custom cellmatch

As the system data.frame cellmatch contains all markers, you can filter interested tissues and cancers to use

e.g., scRNA-data from human blood samples:

# filter cellmatch
cellmatch <- cellmatch[cellmatch$species == "Human", ]
cellmatch <- cellmatch[cellmatch$tissue %in% c("Blood", "Peripheral blood", "Plasma", "Serum", "Umbilical cord blood"), ]

# you can change the content of tissue as "interested"
cellmatch$tissue <- "interested"

# use custom cellmatch by setting tissue as "interested"
obj <- findmarkergene(object = obj,
                      species = "Human",
                      marker = cellmatch,
                      tissue = "interested")

e.g., scRNA-data from human blood samples:

# filter cellmatch
cellmatch <- cellmatch[cellmatch$species == "Human", ]
cellmatch <- cellmatch[cellmatch$tissue %in% c("Blood", "Peripheral blood", "Serum", "Colon", "Colorectum", "Intestine"), ]
cellmatch <- cellmatch[cellmatch$cancer %in% c("Colon Cancer", "Colorectal Cancer"), ]

# you can change the content of tissue and cancer as "interested"
cellmatch$tissue <- "interested"
cellmatch$cancer <- "interested"

# use custom cellmatch by setting tissue and cancer as "interested"
obj <- findmarkergene(object = obj,
                      species = "Human",
                      marker = cellmatch,
                      tissue = "interested",
                      cancer = "interested")
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