getMultiOmicsFeatures: Collect feature mapping for user given databases and omics...

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

Collect feature mapping for user given databases and omics layer.

Description

The functions makes use of the graphite R package to collect pathways from user specified databases. Depending on the omics layer specified, the function extracts either annotated genes/proteins (for transcriptome, proteome layer) or metabolites (for metabolite layer). The data structure that is returned is mandatory to calculate the multi-omics pathway enrichment.

Usage

getMultiOmicsFeatures(
  dbs = c("all"),
  layer = c("all"),
  returnTranscriptome = "SYMBOL",
  returnProteome = "SYMBOL",
  returnMetabolome = "HMDB",
  organism = "hsapiens",
  useLocal = TRUE
)

Arguments

dbs	List of databases that should be queried for pathways. Default: all available databases
layer	List of omics layer that should be addressed. Default: all three layer (transcriptome, proteome, metabolome)
returnTranscriptome	String specifying the returned gene ID format. Default: SYMBOL Options: SYMBOL, ENTREZID, UNIPROT, ENSEMBL, REFSEQ
returnProteome	String specifying the returned protein ID format. Default: SYMBOL Options: SYMBOL, ENTREZID, UNIPROT, ENSEMBL, REFSEQ
returnMetabolome	String specifying the returned metabolite ID format. Default: HMDB Options: HMDB, CAS, DTXCID, DTXSID, SID, CID, ChEBI, KEGG, Drugbank
organism	String specifying the organism of interest. This has direct influence on the available pathway databases. Default: "hsapiens" Options: see getOrganisms
useLocal	Boolean to use local pathway/feature descriptions. In case useLocal is set to FALSE, pathway definitions and feature extraction will be recalculated. This could take several minutes depending on the database used. Pathbank, for example, contains nearly 50000 pathway definition that have to be re-mapped. useLocal has no effect when pathway definitions are retrieved for the first time. Default: TRUE

Value

Nested list with extracted and mapped pathway features.

Examples

getMultiOmicsFeatures(
  dbs = c("kegg"),
  layer = c("transcriptome", "proteome"),
  organism = "hsapiens"
)

getMultiOmicsFeatures(
  dbs = c("kegg", "reactome"),
  layer = c("transcriptome", "metabolome"),
  organism = "mmusculus"
)

getMultiOmicsFeatures(
  dbs = c("reactome"),
  layer = c("proteome"),
  organism = "rnorvegicus",
  returnProteome = "ENTREZID"
)

yigbt/multiGSEA documentation built on Nov. 25, 2024, 9:11 a.m.