Top markers

topMarkers(object, ...)

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

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.

return

character(1). Return type. Uses match.arg() internally and defaults to the first argument in the character vector.

...

Additional arguments.

Value

grouped_df.

See also

Examples

data(seurat_all_markers) x <- topMarkers(seurat_all_markers, n = 2L)
#> Grouping by cluster.
#> Including upregulated markers.
#> Returning as tibble.
#> # A tibble: 6 x 9 #> # Groups: cluster [3] #> cluster name avgLogFC pct1 pct2 pvalue padj geneID geneName #> <fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <chr> <fct> #> 1 0 CD7 2.56 0.528 0.091 8.18e- 6 1.88e- 3 ENSG00000173… CD7 #> 2 0 GNLY 4.78 0.444 0.068 3.27e- 5 7.51e- 3 ENSG00000115… GNLY #> 3 1 S100A8 4.33 0.96 0.091 1.43e-14 3.30e-12 ENSG00000143… S100A8 #> 4 1 TYMP 2.21 1 0.164 4.77e-13 1.10e-10 ENSG00000025… TYMP #> 5 2 HLA-DPB1 1.75 0.947 0.41 2.67e- 8 6.13e- 6 ENSG00000215… HLA-DPB1 #> 6 2 MS4A1 4.53 0.526 0.033 7.53e- 8 1.73e- 5 ENSG00000156… MS4A1