Differential expression per cluster

Usage

diffExpPerCluster(object, ...)

# S4 method for SingleCellExperiment
diffExpPerCluster(object, group, numerator, denominator, ...)

Arguments

object: Object.
group: character(1). Group of interest for differential expression per cluster. Must be a factor column in colData().
numerator: character. Cells to use in the numerator of the contrast (e.g. treatment).
denominator: character. Cells to use in the denominator of the contrast (e.g. control).
...: Passthrough arguments to diffExp().

Value

list containing:

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

Note

Updated 2022-10-25.

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

Examples

data(SingleCellExperiment_Seurat, package = "AcidTest")

## SingleCellExperiment ====
if (goalie::isInstalled("edgeR")) {
    object <- SingleCellExperiment_Seurat
    group <- factor(c("group1", "group2"))
    SummarizedExperiment::colData(object)$group <- group
    suppressMessages({
        x <- diffExpPerCluster(
            object = object,
            group = "group",
            numerator = "group2",
            denominator = "group1",
            caller = "edgeR"
        )
    })
    class(x)
    lapply(x, class)
}
#> $`0`
#> [1] "DGELRT"
#> attr(,"package")
#> [1] "edgeR"
#> 
#> $`1`
#> [1] "DGELRT"
#> attr(,"package")
#> [1] "edgeR"
#> 
#> $`2`
#> [1] "DGELRT"
#> attr(,"package")
#> [1] "edgeR"
#>