Identify oncogenes and tumor suppressor genes from omics data
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Documentation for package ‘Moonlight2R’ version 1.7.0
Help Pages
| confidence | confidence |
| cscape_somatic_output | Cscape-somatic annotations of TCGA-LUAD |
| dataDMA | Output example from the function Driver Mutation Analysis |
| dataFEA | Functional enrichment analysis |
| dataFilt | Gene expression data from TCGA-LUAD |
| dataGLS | Literature search of driver genes |
| dataGMA | Output example from GMA function |
| dataGRN | Gene regulatory network |
| dataGRN_no_noise | Gene regulatory network |
| dataMAF | Mutation data from TCGA LUAD |
| dataMAVISp | MAVISp dataset example |
| dataMethyl | Methylation data matrix from TCGA-LUAD project |
| dataPRA | Output example from function Pattern Recognition Analysis |
| dataURA | Upstream regulator analysis |
| dataURA_plot | Upstream regulator analysis |
| DEGsmatrix | Differentially expressed genes |
| DEG_Methylation_Annotations | Output example from GMA function |
| DEG_Mutations_Annotations | Differentially expressed genes's Mutations |
| DiseaseList | Cancer-related biological processes |
| DMA | DMA |
| EAGenes | Information about genes |
| EncodePromoters | Promoters |
| EpiMix_Results_Regular | Output example from GMA function |
| FEA | FEA |
| GEO_TCGAtab | Information on GEO and TCGA data |
| getDataGEO | getDataGEO |
| GLS | GLS This function carries out gene literature search. |
| GMA | GMA This function carries out Gene Methylation Analysis |
| GRN | Generate network |
| GSEA | GSEA |
| knownDriverGenes | Information of known cancer driver genes from COSMIC |
| LiftMAF | LiftMAF |
| listMoonlight | List of oncogenic mediators of 5 TCGA cancer types |
| loadMAVISp | loadMAVISp |
| LOC_protein | Level of Consequence: Protein |
| LOC_transcription | Level of Consequence: Transcription |
| LOC_translation | Level of Consequence: Translation |
| LPA | LPA |
| LUAD_sample_anno | Sample annotations of TCGA-LUAD project |
| MAFtoCscape | MAFtoCscape |
| MetEvidenceDriver | Methylation evidence table to define driver genes |
| moonlight | moonlight pipeline |
| NCG | Network of Cancer Genes 7.0 |
| Oncogenic_mediators_methylation_summary | Output example from GMA function |
| Oncogenic_mediators_mutation_summary | Oncogenic Mediators Mutation Summary |
| plotCircos | plotCircos |
| plotDMA | plotDMA |
| plotFEA | plotFEA |
| plotGMA | plotGMA This function plots results of the Gene Methylation Analysis. It visualizes the number of hypo/hyper/dual methylated CpG sites in oncogenic mediators or in a user-supplied gene list. The results are visualized either in a single heatmap or split into different ones which is specified in the function's three modes: split, complete and genelist. |
| plotHeatmap | plotHeatmap |
| plotMetExp | plotMetExp This function visualizes results of EpiMix. |
| plotMoonlight | plotMoonlight |
| plotMoonlightMet | plotMoonlightMet This function visualizes the effect of genes on biological processes and total number of hypo/hyper/dual methylated CpG sites in genes. |
| plotNetworkHive | plotNetworkHive: Hive network plot |
| plotURA | plotURA: Upstream regulatory analysis heatmap plot |
| PRA | Pattern Recognition Analysis (PRA) |
| PRAtoTibble | PRAtoTibble |
| RunCscape_somatic | RunCscape_somatic |
| tabGrowBlock | Information of growing/blocking characteristics of 101 biological processes |
| TFinfluence | TFinfluence |
| URA | URA Upstream Regulator Analysis |