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

Updated 2020-01-30.

Examples

data(Seurat, package = "acidtest") ## Seurat ==== object <- Seurat x <- findMarkers(object, caller = "edgeR")
#>
#> ── `findMarkers()` ─────────────────────────────────────────────
#> 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 cell with counts of 1 or more per gene.
#> 230 of 230 genes passed filter.
#> → Applying cell low pass filter.
#> → Running edgeR.
#>
#> ── 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 cell with counts of 1 or more per gene.
#> 230 of 230 genes passed filter.
#> → Applying cell low pass filter.
#> → Running edgeR.
#>
#> ── 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 cell with counts of 1 or more per gene.
#> 230 of 230 genes passed filter.
#> → Applying cell low pass filter.
#> → Running edgeR.
#> [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" #>