findMarkers: Find cluster-specific marker genes

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

Find cluster-specific marker genes

Description

Find cluster-specific marker genes

Usage

findMarkers(object, ...)

## S4 method for signature '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)
}

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