getFeatures: Wrapper to extract features (nodes) from given pathways.

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

Wrapper to extract features (nodes) from given pathways.

Description

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.

Usage

getFeatures(
  pathway,
  which = "proteins",
  org = "hsapiens",
  returntype = "SYMBOL"
)

Arguments

pathway	A pathway created with pathways command.
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

Value

Feature list with gene symbols (genes/proteins) or CHEBI IDs (metabolites)

Examples

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")[[1]]
getFeatures(pathways, which = "proteins", org = "mmusculus", returntype = "SYMBOL")

yigbt/multiGSEA documentation built on Oct. 31, 2024, 2:22 p.m.