Top markers

topMarkers(object, ...)

# S4 method for SeuratMarkersPerCluster
topMarkers(object, n = 10L, direction = c("up", "down", "both"))

Arguments

object

Object.

n

integer(1). Number of genes per cluster.

direction

character(1). Whether to include upregulated ("up"; positive LFC), downregulated ("down"; negative LFC) or "both" directions of association per cluster.

...

Additional arguments.

Value

DataFrame.

Note

Updated 2020-01-30.

Examples

data(seurat_all_markers) ## SeuratMarkersPerCluster ==== object <- seurat_all_markers x <- topMarkers(object, n = 2L)
#> Including upregulated markers.
#> DataFrame with 6 rows and 9 columns #> avgLogFC cluster name padj pct1 pct2 #> <numeric> <factor> <factor> <numeric> <numeric> <numeric> #> 1 2.55597346986167 0 CD7 0.00188111817515741 0.528 0.091 #> 2 4.78418517067847 0 GNLY 0.00751104550006906 0.444 0.068 #> 3 4.3281839079057 1 S100A8 3.29657014438234e-12 0.96 0.091 #> 4 2.21103115611057 1 TYMP 1.09779336517925e-10 1 0.164 #> 5 1.74909415488556 2 HLA-DPB1 6.13422830445816e-06 0.947 0.41 #> 6 4.533789508485 2 MS4A1 1.73242659304758e-05 0.526 0.033 #> pvalue geneID geneName #> <numeric> <factor> <factor> #> 1 8.17877467459745e-06 ENSG00000173762 CD7 #> 2 3.26567195655177e-05 ENSG00000115523 GNLY #> 3 1.43329136712276e-14 ENSG00000143546 S100A8 #> 4 4.77301463121415e-13 ENSG00000025708 TYMP #> 5 2.66705578454703e-08 ENSG00000215048 HLA-DPB1 #> 6 7.53228953498949e-08 ENSG00000156738 MS4A1