Find cluster-specific marker genes

findMarkers(object, ...)

# S4 method for SingleCellExperiment
findMarkers(object, ...)

# S4 method for Seurat
findMarkers(object, ...)

Arguments

object

Object.

...

Passthrough arguments to diffExp().

Value

list containing:

  • caller = "edgeR": DGELRT.

  • caller = "DESeq2": DESeqResults.

Note

Cluster identity (ident) must be defined in colData() for this function to work.

Examples

data(seurat) x <- findMarkers(seurat, caller = "edgeR")
#> 3 clusters detected
#> Cluster 0 ====
#> Performing differential expression with edgeR.
#> Total: 80 cells #> Numerator: 36 cells #> Denominator: 44 cells
#> Applying gene expression low pass filter.
#> Requiring at least 1 cells with counts of 1 or more per gene.
#> 230 of 230 genes passed filter.
#> Running edgeR.
#> user system elapsed #> 0.404 0.012 0.464
#> Cluster 1 ====
#> Performing differential expression with edgeR.
#> Total: 80 cells #> Numerator: 25 cells #> Denominator: 55 cells
#> Applying gene expression low pass filter.
#> Requiring at least 1 cells with counts of 1 or more per gene.
#> 230 of 230 genes passed filter.
#> Running edgeR.
#> user system elapsed #> 0.424 0.012 0.479
#> Cluster 2 ====
#> Performing differential expression with edgeR.
#> Total: 80 cells #> Numerator: 19 cells #> Denominator: 61 cells
#> Applying gene expression low pass filter.
#> Requiring at least 1 cells with counts of 1 or more per gene.
#> 230 of 230 genes passed filter.
#> Running edgeR.
#> user system elapsed #> 0.365 0.010 0.414
#> [1] "list"
lapply(x, class)
#> $`0` #> [1] "DGELRT" #> attr(,"package") #> [1] "edgeR" #> #> $`1` #> [1] "DGELRT" #> attr(,"package") #> [1] "edgeR" #> #> $`2` #> [1] "DGELRT" #> attr(,"package") #> [1] "edgeR" #>