Man pages for ppdragondw/Key2Enrich
R package of gene set enrichment analysis
| childIsEntry | childIsEntry |
| formatInputSample | Format input file to dataframe class with entrez ID, symbol... |
| getAllGeneInPathwayDF | Get all KEGG pathway ID and its corresponding gene list in... |
| getAllPathNameAndID | Get all KEGG pathway name and ID of species |
| getAllTypesID | Convert input file ID to dataframe class with entrez ID,... |
| getColor | Get color for node from log fold change value |
| getGeneInOnePathwayDF | Get gene list in specific KEGG pathway |
| getGeneSymbol | Get gene symbol from different species |
| getIndex | Get index of value in array for right color key |
| getIndex2 | Get index of value in array for left color key |
| get_inputSampleKEGG_m | Get sample genes in specific KEGG pathway |
| get_n | Get the number of sample genes with KEGG gene ID |
| getN | Get the number of all genes with KEGG gene ID |
| getPathInfo | Get KEGG pathway info from xmlRoot |
| getPValue | Calculate p-value and adjust p-value of KEGG pathway on input... |
| getTotalPathNames | Get all KEGG pathway name for species |
| GO2Enrich | Perform Gene Ontology enrichment analysis |
| gs | Sample in GSEABase class |
| inputSample | Data from sample file |
| KEGGEnricherMatrixRealTime | Get enrichment output matrix of enriched KEGG pathway |
| KEGGID2EntrezID | Get all KEGG gene ID and entrezgene ID in a specific species |
| Key2EnrichBarplot | Plot barplot |
| Key2KEGGEnrich | Performe enrichment analysis based on KEGG pathway, plot... |
| mappingOnSpecifiedKEGGPathway | Download KEGG pathway files and mapping genes on pathway |
| multiplot | Plot two image on same panel |
| parseEntry | parseEntry |
| parseGraphic | Get info from list class of graphic info |
| parseKGMLFile | Read XML file |
| parseList2Dataframe | Convert list class of node info to dataframe |
| plotGradient | Plot heatmap color key for node |
| plotSigImg | Plot heat map rectangle on the KEGG pathway node |
| Reactome2Enrich | Get enrichment matrix of enriched Reactome pathway |
| readInputFile | Read samples files with different annotation ID |
| sampleWith3IDs | Mapping input file with ID to symbol, entrez, ensembl IDs |
| speciesConvert2Biomart | Convert input species to biomart species |
| speciesKEGGConvert | Convert input species to KEGG species |
| speciesKEGGFlagConvert | Convert input species to KEGG species with flag |
| textStamp | Add text stamp on image |
