iSEEnrich

iSEEnrich() creates an initial state of an iSEE instance for interactive exploration of feature sets extracted from GO and KEGG database, displaying all associated genes in a RowDataTable panel.

Usage

iSEEnrich(
  sce,
  collection = c("GO", "KEGG"),
  organism = "org.Hs.eg.db",
  gene_identifier = "ENTREZID",
  clusters = colnames(colData(sce))[1],
  groups = colnames(colData(sce))[1],
  reddim_type = "PCA"
)

Arguments

sce

SingleCellExperiment object

collection

A character vector specifying the gene set collections of interest (GO,KEGG)

organism

A character string of the org.*.eg.db package to use to extract mappings of gene sets to gene IDs.

gene_identifier

A character string specifying the identifier to use to extract gene IDs for the organism package

clusters

A character string containing the name of the clusters/cell-type/state...(as listed in the colData of the sce)

groups

A character string of the groups/conditions...(as it appears in the colData of the sce)

reddim_type

A string vector containing the dimensionality reduction type

Value

A list of "Panel" objects specifying the initial state of iSEE instance

Examples

sce <- scRNAseq::RichardTCellData()
#> snapshotDate(): 2024-10-04
#> loading from cache
sce <- scuttle::logNormCounts(sce)
sce <- scater::runPCA(sce)
GO_collection <- "GO"
Mm_organism <- "org.Mm.eg.db"
gene_id <- "SYMBOL"
clusters <- "stimulus"
groups <- "single cell quality"
reddim_type <- "PCA"
results <- iSEEnrich(sce = sce,
                     collection = GO_collection,
                     organism = Mm_organism,
                     gene_identifier = gene_id,
                     clusters = clusters,
                     groups = groups,
                     reddim_type = reddim_type)