% Generated by roxygen2: do not edit by hand % Please edit documentation in R/importGeneSets.R \name{importGeneSetsFromMSigDB} \alias{importGeneSetsFromMSigDB} \title{Imports gene sets from MSigDB} \usage{ importGeneSetsFromMSigDB( inSCE, categoryIDs = "H", species = "Homo sapiens", mapping = c("gene_symbol", "human_gene_symbol", "entrez_gene"), by = "rownames", verbose = TRUE, noMatchError = TRUE ) } \arguments{ \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.} \item{categoryIDs}{Character vector containing the MSigDB gene set ids. The column \code{ID} in the table returned by \code{getMSigDBTable()} shows the list of possible gene set IDs that can be obtained. Default is \code{"H"}.} \item{species}{Character. Species available can be found using the function \code{\link[msigdbr]{msigdbr_species}}. Default \code{"Homo sapiens"}.} \item{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 \code{by} parameter must be either in gene symbol or Entrez gene id format to match IDs from MSigDB.} \item{by}{Character. Describes the location within \code{inSCE} where the gene identifiers in the MSigDB gene sets should be mapped. If set to \code{"rownames"} then the features will be searched for among \code{rownames(inSCE)}. This can also be set to one of the column names of \code{rowData(inSCE)} in which case the gene identifies will be mapped to that column in the \code{rowData} of \code{inSCE}. See \link{featureIndex} for more information. Default \code{"rownames"}.} \item{verbose}{Boolean. Whether to display progress. Default \code{TRUE}.} \item{noMatchError}{Boolean. Show an error if a collection does not have any matching features. Default \code{TRUE}.} } \value{ A \link[SingleCellExperiment]{SingleCellExperiment} object with gene set from \code{collectionName} output stored to the \link{metadata} slot. } \description{ Gets a list of MSigDB gene sets stores it in the metadata of the \linkS4class{SingleCellExperiment} object. These gene sets can be used in downstream quality control and analysis functions in \link{singleCellTK}. } \details{ The gene identifiers in gene sets from MSigDB will be retrieved using the \code{\link{msigdbr}} package. They will be mapped to the IDs in \code{inSCE} using the \code{by} parameter and stored in a \linkS4class{GeneSetCollection} object from package \link{GSEABase}. This object is stored in \code{metadata(inSCE)$sctk$genesets}, which can be accessed in downstream analysis functions such as \link[singleCellTK]{runCellQC}. } \examples{ data(scExample) sce <- importGeneSetsFromMSigDB(inSCE = sce, categoryIDs = "H", species = "Homo sapiens", mapping = "gene_symbol", by = "feature_name") } \seealso{ \link{importGeneSetsFromList} for importing from lists, \link{importGeneSetsFromGMT} for importing from GMT files, and \linkS4class{GeneSetCollection} objects. } \author{ Joshua D. Campbell }