importGeneSetsFromList: Imports gene sets from a list
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description Usage Arguments Details Value Author(s) See Also Examples

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.

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

`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"`.

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.

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

Joshua D. Campbell

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

data(scExample)

# Generate gene sets from 'rownames'
gs1 <- rownames(sce)[1:10]
gs2 <- rownames(sce)[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")