getFeatures {multiGSEA} | R Documentation |
Function to extract the features (nodes) from a given list of pathways. These
pathways have to be compiled with the
pathways
function. Features can only be
extracted for \'proteins\' or \'metabolites\'. Features will by default be
mapped to gene symbols.
getFeatures( pathway, which = "proteins", org = "hsapiens", returntype = "SYMBOL" )
pathway |
A pathway created with |
which |
Mode to extract the features, either \'proteins\' or \'metabolites\'. |
org |
String specifying the organism, which is necessary for featureID mapping. Default: human |
returntype |
String that specifies the returning ID type. Default: SYMBOL Options (genes/proteins): SYMBOL, ENTREZID, UNIPROT, ENSEMBL, REFSEQ Options (metabolites): HMDB, CAS, DTXCID, DTXSID, SID, CID, ChEBI, KEGG, Drugbank |
Feature list with gene symbols (genes/proteins) or CHEBI IDs (metabolites)
pathways <- graphite::pathways("hsapiens", "kegg")[[1]] getFeatures(pathways) pathways <- graphite::pathways("mmusculus", "kegg")[[1]] getFeatures(pathways, which = "metabolites", org = "mmusculus", returntype = "HMDB") pathways <- graphite::pathways("mmusculus", "kegg") getFeatures(pathways, which = "proteins", org = "mmusculus", returntype = "SYMBOL")