FindConservedMarkers: Finds markers that are conserved between the two groups

In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

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	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.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
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)

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.