getGeneMapping: Mapping between pathway encoded genes/proteins and different...

In multiGSEA: Combining GSEA-based pathway enrichment with multi omics data integration

Description

Function to retrieve the gene/protein identifier mapping. Ongoing from genes/proteins retrieved from pathway definitions, which often include two or more ID formats or a format that is not present in your omics measurement, this function maps those IDs to a given format. Depending on the organism, additional packages have to be installed.

Usage

getGeneMapping(features, keytype, org = "hsapiens", returntype = "SYMBOL")

Arguments

features	List of identifiers to be mapped.
keytype	String specifying the ID type, e.g., "ENTREZID" or "UNIPROT".
org	String that defines the organism. Default: hsapiens Options: see getOrganisms
returntype	String that specifies the returning ID type. Default: SYMBOL, Options: SYMBOL, ENTREZID, UNIPROT, ENSEMBL, REFSEQ

Value

List containing mapped gene/protein IDs.

Examples

features <- graphite::nodes(graphite::pathways("hsapiens", "kegg")[[1]])
features <- gsub("ENTREZID:", "", features)
keytype <- "ENTREZID"
getGeneMapping(features, keytype)

getGeneMapping(features, keytype, returntype = "UNIPROT")

features <- graphite::nodes(graphite::pathways("rnorvegicus", "reactome")[[1]])
features <- gsub("UNIPROT:", "", features)
getGeneMapping(features, keytype = "UNIPROT", org = "rnorvegicus")

getGeneMapping(features,
    keytype = "UNIPROT",
    org = "rnorvegicus",
    returntype = "ENSEMBL"
)

multiGSEA documentation built on Nov. 8, 2020, 8:15 p.m.