Combining GSEA-based pathway enrichment with multi omics data integration

Documentation for package ‘multiGSEA’ version 1.17.3

archiveDir	Retrieve the path to the cache directory.
archivePath	Retrieve path to a cached file.
combinePvalues	Calculate a combined p-value for multiple omics layer.
extractPvalues	Create a reshaped data frame from multiGSEA output.
getFeatures	Wrapper to extract features (nodes) from given pathways.
getGeneMapping	Mapping between pathway encoded genes/proteins and different ID formats.
getIDMappingDatabase	Get the correct ID mapping database
getMappedFeatures	Wrapper to get feature mappings.
getMetaboliteIDformats	Helper function to get all different metabolite ID formats
getMetaboliteMapping	Mapping between pathway encoded metabolites and different metabolite ID formats.
getMultiOmicsFeatures	Collect feature mapping for user given databases and omics layer.
getOrganisms	Get list of supported organisms
initOmicsDataStructure	Create an empty data structure for measured omics features
loadLocal	Read a local RDS file.
mapIDType	Helper function to map only a subset of metabolite IDs
metabolome	Metabolomic data set that is used in the toy example provided by the 'multiGSEA' package.
multiGSEA	Calculate pathway enrichment for multiple omics layer.
proteome	Proteomic data set that is used in the toy example provided by the 'multiGSEA' package.
rankFeatures	Pre-rank features prior to calculating enrichment scores.
rename_duplicates	Make a list of strings unique
transcriptome	Transcriptomic data set that is used in the toy example provided by the 'multiGSEA' package.