# Identify oncogenes and tumor suppressor genes from omics data

## Documentation for package ‘Moonlight2R’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
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
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
URA | URA Upstream Regulator Analysis