Seurat (version 4.3.0.1)

FindConservedMarkers: Finds markers that are conserved between the groups

Description

Finds markers that are conserved between the groups

Usage

FindConservedMarkers(
  object,
  ident.1,
  ident.2 = NULL,
  grouping.var,
  assay = "RNA",
  slot = "data",
  min.cells.group = 3,
  meta.method = metap::minimump,
  verbose = TRUE,
  ...
)

Value

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.

Arguments

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 test.use is "negbinom", "poisson", or "DESeq2", slot will be set to "counts"

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

Examples

if (FALSE) {
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")
}