confidence              confidence
cscape_somatic_output   Cscape-somatic annotations of TCGA-LUAD
DAPsmatrix              Differentially abundant proteins
dataDMA                 Output example from the function Driver
                        Mutation Analysis
dataFEA                 Functional enrichment analysis with ORA method
dataFEA_fgsea           Functional enrichment analysis with fgsea
                        method
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
DEG_Methylation_Annotations
                        Output example from GMA function
DEG_Mutations_Annotations
                        Differentially expressed genes's Mutations
DEGsmatrix              Differentially expressed genes
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
