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Seurat (version 2.1.0)

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", ...)

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)

…

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 (fisher_pval), percentage of cells expressing the marker, average differences)

Examples

Run this code
# 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 = 1, ident.2 = 2, grouping.var = "groups")

# }

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