diffExpPerCluster: Differential expression per cluster

In acidgenomics/r-acidsinglecell: Acid Genomics Single Cell Experiment

Differential expression per cluster

Description

Differential expression per cluster

Usage

diffExpPerCluster(object, ...)

## S4 method for signature '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)
}

acidgenomics/r-acidsinglecell documentation built on March 30, 2024, 5:39 a.m.