Finds markers that are conserved between the two groups
FindConservedMarkers(object, ident.1, ident.2 = NULL, grouping.var,
assay.type = "RNA", meta.method = minimump, ...)Seurat object
Identity class to define markers for
A second identity class for comparison. If NULL (default) - use all other cells for comparison.
grouping variable
Type of assay to fetch data for (default is RNA)
method for combining p-values. Should be a function from the metap package (NOTE: pass the function, not a string)
parameters to pass to FindMarkers
Matrix containing a ranked list of putative conserved markers, and associated statistics (p-values within each group and a combined p-value (such as Fishers combined p-value or others from the MetaDE package), percentage of cells expressing the marker, average differences)
# NOT RUN {
pbmc_small
# Create a simulated grouping variable
pbmc_small@meta.data$groups <- sample(
x = c("g1", "g2"),
size = length(x = pbmc_small@cell.names),
replace = TRUE
)
FindConservedMarkers(pbmc_small, ident.1 = 0, ident.2 = 1, grouping.var = "groups")
# }
# NOT RUN {
# }
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