RESET (version 1.0.0)

resetForSeurat: RESET wrapper for scRNA-seq data processed using the Seurat framework

Description

Executes the Reconstruction Set Test (RESET) method (reset) on normalized scRNA-seq data stored in a Seurat object. Will analyze the normalized counts in the active assay (i.e., either the log-normalized or SCTransformed counts).

Usage

resetForSeurat(seurat.data, num.pcs, gene.set.collection, k=10, random.threshold, 
               k.buff=0, q=0, test.dist="normal", norm.type="2", per.var=FALSE)

Value

An updated Seurat object with the following modifications:

• RESET sample-level gene set score matrix S stored in the "data" slot of a new "RESET" Assay object.

• RESET overall gene set scores stored in the feature metadata column "RESET".

Arguments

seurat.data

The Seurat object that holds the scRNA-seq data. Assumes PCA has already been performed on a centered and scaled version of the normalized counts.

num.pcs

Number of PCs to use in the RESET method. If not specified, will use all computed PCs. The projection of the scRNA-seq data onto these PCs will be used as the X.test matrix for the reset call.

gene.set.collection

List of m gene sets for which scores are computed. Each element in the list corresponds to a gene set and the list element is a vector of indices for the genes in the set. The index value is defined relative to the order of genes in the Seurat active assay. Gene set names should be specified as list names. See createVarSetCollection for utility function that can be used to help generate this list of indices.

k

See description in reset

random.threshold

See description in reset

k.buff

See description in reset

q

See description in reset

test.dist

See description in reset

norm.type

See description in reset

per.var

See description in reset

See Also

reset,createVarSetCollection

Examples

    # Only run example code if Seurat package is available
    if (requireNamespace("Seurat", quietly=TRUE) & requireNamespace("SeuratObject", quietly=TRUE)) {
        # Define a collection with three gene sets
        collection=list(set1=1:10, set2=11:20, set3=21:30)
        # Execute on the pbmc_small scRNA-seq data set included with SeuratObject
        # See vignettes for more detailed Seurat examples
        reset.out = resetForSeurat(seurat.data=SeuratObject::pbmc_small,
            num.pcs=5,
            gene.set.collection=collection)
        # Retrieve the scores for the first 10 cells
        reset.out@assays$RESET[,1:10]
        # Retrieve the overall scores
        reset.out@assays$[e-mail]
    }