importGeneSetsFromList {singleCellTK} | R Documentation

## Imports gene sets from a list

### Description

Converts a list of gene sets into a GeneSetCollection and stores it in the metadata of the SingleCellExperiment object. These gene sets can be used in downstream quality control and analysis functions in singleCellTK.

### Usage

    importGeneSetsFromList(
      inSCE,
      geneSetList,
      collectionName = "GeneSetCollection",
      by = "rownames"
    )

### Arguments

`inSCE` | Input SingleCellExperiment object.
`geneSetList` | Named List. A list containing one or more gene sets. Each element of the list should be a character vector of gene identifiers. The names of the list will be become the gene set names in the GeneSetCollection object.
`collectionName` | Character. Name of collection to add gene sets to. If this collection already exists in `inSCE`, then these gene sets will be added to that collection. Any gene sets within the collection with the same name will be overwritten. Default `GeneSetCollection`.
`by` | Character or character vector. Describes the location within `inSCE` where the gene identifiers in `geneSetList` should be mapped. If set to `"rownames"` then the features will be searched for among `rownames(inSCE)`. This can also be set to one of the column names of `rowData(inSCE)` in which case the gene identifies will be mapped to that column in the `rowData` of `inSCE`. Finally, `by` can be a vector the same length as the number of gene sets in `geneSetList` and the elements of the vector can point to different locations within `inSCE`. See featureIndex for more information. Default `"rownames"`.

### Details

The gene identifiers in gene sets in `geneSetList` will be mapped to the rownames of `inSCE` using the `by` parameter and stored in a GeneSetCollection object from package GSEABase. This object is stored in `metadata(inSCE)$sctk$genesets`, which can be accessed in downstream analysis functions such as runCellQC.

### Value

A SingleCellExperiment object with gene set from `collectionName` output stored to the metadata slot.

### Author(s)

Joshua D. Campbell

### See Also

importGeneSetsFromCollection for importing from GeneSetCollection objects, importGeneSetsFromGMT for importing from GMT files, and importGeneSetsFromMSigDB for importing MSigDB gene sets.

### Examples

    data(scExample)

    # Generate gene sets from 'rownames'
    gs1 <- rownames(sce)[seq(10)]
    gs2 <- rownames(sce)[seq(11,20)]
    gs <- list("geneset1" = gs1, "geneset2" = gs2)
    sce <- importGeneSetsFromList(inSCE = sce,
                                  geneSetList = gs,
                                  by = "rownames")

    # Generate a gene set for mitochondrial genes using
    # Gene Symbols stored in 'rowData'
    mito.ix <- grep("^MT-", rowData(sce)$feature_name)
    mito <- list(mito = rowData(sce)$feature_name[mito.ix])
    sce <- importGeneSetsFromList(inSCE = sce,
                                 geneSetList = mito,
                                 by = "feature_name")

[Package singleCellTK version 2.2.0 Index]