Load gene sets annotation data — get

This function loads annotation data from RDS files located in the inst/extdata/geneSets directory of the package. If the specified file does not exist locally, it will be downloaded from the GitHub repository.

Usage

get_annoData(
  type = c("CellTypes_Lake2018", "CellTypes_Martins2021", "CellTypes_Seidlitz2020",
    "DGN", "GO_BP", "GO_CC", "GO_MF", "KEGG", "Reactome", "SynGO", "WikiPathways",
    "MeSH_A", "MeSH_B", "MeSH_C", "MeSH_D", "MeSH_E", "MeSH_F", "MeSH_G", "MeSH_H",
    "MeSH_I", "MeSH_J", "MeSH_K", "MeSH_L", "MeSH_M", "MeSH_N", "MeSH_Z")
)

Arguments

type

A character string specifying the type of gene set to load. Options are:

"CellTypes_Lake2018": Cell types data from Lake2018
"CellTypes_Martins2021": Cell types data from Martins2021
"CellTypes_Seidlitz2020": Cell types data from Seidlitz2020
"DGN": DisGeNET gene sets
"GO_BP": Gene Ontology Biological Process
"GO_CC": Gene Ontology Cellular Component
"GO_MF": Gene Ontology Molecular Function
"KEGG": KEGG gene sets
"Reactome": Reactome gene sets
"SynGO": SynGO gene sets
"WikiPathways": WikiPathways gene sets
"MeSH_A": MeSH category A gene sets
"MeSH_B": MeSH category B gene sets
"MeSH_C": MeSH category C gene sets
"MeSH_D": MeSH category D gene sets
"MeSH_E": MeSH category E gene sets
"MeSH_F": MeSH category F gene sets
"MeSH_G": MeSH category G gene sets
"MeSH_H": MeSH category H gene sets
"MeSH_I": MeSH category I gene sets
"MeSH_J": MeSH category J gene sets
"MeSH_K": MeSH category K gene sets
"MeSH_L": MeSH category L gene sets
"MeSH_M": MeSH category M gene sets
"MeSH_N": MeSH category N gene sets
"MeSH_Z": MeSH category Z gene sets

Value

A data frame containing the annotation data.

Examples

if (FALSE) { # \dontrun{
annoData <- get_annoData("GO_BP")
} # }