importGeneSetsFromMSigDB: Imports gene sets from MSigDB
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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

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

importGeneSetsFromMSigDB(
  inSCE,
  categoryIDs,
  species = "Homo sapiens",
  mapping = c("gene_symbol", "human_gene_symbol", "entrez_gene"),
  by = "rownames",
  verbose = TRUE
)

`inSCE`	Input SingleCellExperiment object.
`categoryIDs`	Character vector containing the MSigDB gene set ids. The column `ID` in the table returned by `getMSigDBTable()` shows the list of possible gene set IDs that can be obtained.
`species`	Character. Species available can be found using the function `msigdbr_show_species`. Default `"Homo sapiens"`.
`mapping`	Character. One of "gene_symbol", "human_gene_symbol", or "entrez_gene". Gene identifiers to be used for MSigDB gene sets. IDs denoted by the `by` parameter must be either in gene symbol or Entrez gene id format to match IDs from MSigDB.
`by`	Character. Describes the location within `inSCE` where the gene identifiers in the MSigDB gene sets 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`. See featureIndex for more information. Default `"rownames"`.
`verbose`	Boolean. Whether to display progress. Default `TRUE`.

The gene identifiers in gene sets from MSigDB will be retrieved using the msigdbr package. They will be mapped to the IDs in 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

importGeneSetsFromList for importing from lists, importGeneSetsFromGMT for importing from GMT files, and GeneSetCollection objects.

data(scExample)
sce <- importGeneSetsFromMSigDB(inSCE = sce,
                                categoryIDs = "H",
                                species = "Homo sapiens",
                                mapping = "gene_symbol",
                                by = "feature_name")