Man pages for yigbt/multiGSEA
Combining GSEA-based pathway enrichment with multi omics data integration
| 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... |
| 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... |
| getMultiOmicsFeatures | Collect feature mapping for user given databases and omics... |
| 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... |
| multiGSEA | Calculate pathway enrichment for multiple omics layer. |
| proteome | Proteomic data set that is used in the toy example provided... |
| 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... |
