Finds markers that are conserved between the groups
Finds markers that are conserved between the groups
FindConservedMarkers( object, ident.1, ident.2 = NULL, grouping.var, assay = "RNA", slot = "data", 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 |
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.