% 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"

)

}

}