Seurat (version 2.3.4)

FindConservedMarkers: Finds markers that are conserved between the two groups

Description

Finds markers that are conserved between the two groups

Usage

FindConservedMarkers(object, ident.1, ident.2 = NULL, grouping.var,
  assay.type = "RNA", meta.method = minimump, ...)

Arguments

object

Seurat 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.type

Type of assay to fetch data for (default is RNA)

meta.method

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

Value

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)

Examples

# NOT RUN {
pbmc_small
# Create a simulated grouping variable
[e-mail]$groups <- sample(
  x = c("g1", "g2"),
  size = length(x = [e-mail]),
  replace = TRUE
)
FindConservedMarkers(pbmc_small, ident.1 = 0, ident.2 = 1, grouping.var = "groups")
# }
# NOT RUN {
# }