Find cluster-specific marker genes

Usage

findMarkers(object, ...)

# S4 method for SingleCellExperiment
findMarkers(object, clusters = NULL, ...)

Arguments

object: Object.
clusters: character or NULL. Cluster identifiers. Must correspond to values in clusters(). Note that Seurat uses zero-indexed IDs by default (e.g. 0, 1, 2, ...). If left NULL (default), all clusters will be analyzed. Looping across clusters manually here can avoid memory issues on laptops and other machines with limited amounts of RAM.
...: Passthrough arguments to diffExp().

Value

list containing:

caller = "edgeR": DGELRT.
caller = "DESeq2": DESeqResults.

Note

Updated 2021-09-13.

Examples

data(SingleCellExperiment_Seurat, package = "AcidTest")

## SingleCellExperiment ====
if (goalie::isInstalled("edgeR")) {
    object <- SingleCellExperiment_Seurat
    x <- findMarkers(object, caller = "edgeR")
    class(x)
    lapply(x, class)
}
#> → Finding markers.
#> ℹ 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.
#> ℹ Requiring at least 1 cell with counts of 1 or more per gene.
#> ℹ 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.
#> ℹ Requiring at least 1 cell with counts of 1 or more per gene.
#> ℹ 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.
#> ℹ Requiring at least 1 cell with counts of 1 or more per gene.
#> ℹ 230 of 230 genes passed filter.
#> → Applying cell low pass filter.
#> → Running edgeR.
#> $`0`
#> [1] "DGELRT"
#> attr(,"package")
#> [1] "edgeR"
#> 
#> $`1`
#> [1] "DGELRT"
#> attr(,"package")
#> [1] "edgeR"
#> 
#> $`2`
#> [1] "DGELRT"
#> attr(,"package")
#> [1] "edgeR"
#>