View source: R/differential_expression.R
FindConservedMarkers | R Documentation |
Finds markers that are conserved between the groups
FindConservedMarkers(
object,
ident.1,
ident.2 = NULL,
grouping.var,
assay = "RNA",
slot = "data",
min.cells.group = 3,
meta.method = metap::minimump,
verbose = TRUE,
...
)
object |
An object |
ident.1 |
Identity class to define markers for |
ident.2 |
A second identity class for comparison. If NULL (default) - use all other cells for comparison. |
grouping.var |
grouping variable |
assay |
of assay to fetch data for (default is RNA) |
slot |
Slot to pull data from; note that if |
min.cells.group |
Minimum number of cells in one of the groups |
meta.method |
method for combining p-values. Should be a function from the metap package (NOTE: pass the function, not a string) |
verbose |
Print a progress bar once expression testing begins |
... |
parameters to pass to FindMarkers |
data.frame 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 metap package), percentage of cells expressing the marker, average differences). Name of group is appended to each associated output column (e.g. CTRL_p_val). If only one group is tested in the grouping.var, max and combined p-values are not returned.
## Not run:
data("pbmc_small")
pbmc_small
# Create a simulated grouping variable
pbmc_small[['groups']] <- sample(x = c('g1', 'g2'), size = ncol(x = pbmc_small), replace = TRUE)
FindConservedMarkers(pbmc_small, ident.1 = 0, ident.2 = 1, grouping.var = "groups")
## End(Not run)
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