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+++ b/man/getMultiOmicsFeatures.Rd
@@ -0,0 +1,76 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature_processing.R
+\name{getMultiOmicsFeatures}
+\alias{getMultiOmicsFeatures}
+\title{Collect feature mapping for user given databases and omics layer.}
+\usage{
+getMultiOmicsFeatures(
+  dbs = c("all"),
+  layer = c("all"),
+  returnTranscriptome = "SYMBOL",
+  returnProteome = "SYMBOL",
+  returnMetabolome = "HMDB",
+  organism = "hsapiens",
+  useLocal = TRUE
+)
+}
+\arguments{
+\item{dbs}{List of databases that should be queried for pathways. Default:
+all available databases}
+
+\item{layer}{List of omics layer that should be addressed. Default: all three
+layer (transcriptome, proteome, metabolome)}
+
+\item{returnTranscriptome}{String specifying the returned gene ID format.
+Default: SYMBOL Options: SYMBOL, ENTREZID, UNIPROT, ENSEMBL, REFSEQ}
+
+\item{returnProteome}{String specifying the returned protein ID format.
+Default: SYMBOL Options: SYMBOL, ENTREZID, UNIPROT, ENSEMBL, REFSEQ}
+
+\item{returnMetabolome}{String specifying the returned metabolite ID format.
+Default: HMDB Options: HMDB, CAS, DTXCID, DTXSID, SID, CID, ChEBI, KEGG, Drugbank}
+
+\item{organism}{String specifying the organism of interest. This has direct
+influence on the available pathway databases. Default: "hsapiens"
+Options: see \code{\link[multiGSEA]{getOrganisms}}}
+
+\item{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.
+}
+\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.
+}
+\examples{
+
+getMultiOmicsFeatures(
+  dbs = c("kegg"),
+  layer = c("transcriptome", "proteome"),
+  organism = "hsapiens"
+)
+\donttest{
+getMultiOmicsFeatures(
+  dbs = c("kegg", "reactome"),
+  layer = c("transcriptome", "metabolome"),
+  organism = "mmusculus"
+)
+
+getMultiOmicsFeatures(
+  dbs = c("reactome"),
+  layer = c("proteome"),
+  organism = "rnorvegicus",
+  returnProteome = "ENTREZID"
+)
+}
+}