Top markers

Top markers

Usage

topMarkers(object, ...)

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

Arguments

object

Object.

direction

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

n

integer(1). Number of genes per cluster.

...

Additional arguments.

Value

DataFrame.

Note

Updated 2022-06-09.

Examples

data(SeuratMarkersPerCluster, package = "AcidTest")

## SeuratMarkersPerCluster ====
object <- SeuratMarkersPerCluster
x <- topMarkers(
    object = object,
    direction = "up",
    n = 2L
)
#> ℹ Including upregulated markers.
print(x)
#> DataFrame with 6 rows and 9 columns
#>   avgLog2Fc  cluster     name        padj      pct1      pct2      pvalue
#>   <numeric> <factor> <factor>   <numeric> <numeric> <numeric>   <numeric>
#> 1   3.86502        0 CD7      1.88112e-03     0.528     0.091 8.17877e-06
#> 2   7.52625        0 GNLY     7.51105e-03     0.444     0.068 3.26567e-05
#> 3   6.56570        1 S100A8   3.29657e-12     0.960     0.091 1.43329e-14
#> 4   3.28007        1 TYMP     1.09779e-10     1.000     0.164 4.77301e-13
#> 5   2.53369        2 HLA-DPB1 6.13423e-06     0.947     0.410 2.66706e-08
#> 6   7.49201        2 MS4A1    1.73243e-05     0.526     0.033 7.53229e-08
#>            geneId geneName
#>          <factor> <factor>
#> 1 ENSG00000173762 CD7     
#> 2 ENSG00000115523 GNLY    
#> 3 ENSG00000143546 S100A8  
#> 4 ENSG00000025708 TYMP    
#> 5 ENSG00000223865 HLA-DPB1
#> 6 ENSG00000156738 MS4A1