EG                      Definition for S3 class 'EG'
GS                      Definition for S3 class 'GS'
aOnto                   Definition for S3 class 'aOnto'
cTarget                 Definition for S3 class 'cTarget'
dTarget                 Definition for S3 class 'dTarget'
eGSEA                   Definition for S3 class 'eGSEA'
eTarget                 Definition for S3 class 'eTarget'
eTerm                   Definition for S3 class 'eTerm'
iSubg                   Definition for S3 class 'iSubg'
ls_eTerm                Definition for S3 class 'ls_eTerm'
pNode                   Definition for S3 class 'pNode'
pPerf                   Definition for S3 class 'pPerf'
sGS                     Definition for S3 class 'sGS'
sTarget                 Definition for S3 class 'sTarget'
xAggregate              Function to aggregate data respecting number of
                        features
xCheckParallel          Function to check whether parallel computing
                        should be used and how
xCircos                 Function to visualise a network as a circos
                        plot
xColormap               Function to define a colormap
xCombineNet             Function to combine networks from a list of
                        igraph objects
xContour                Function to visualise a numeric matrix as a
                        contour plot
xCorrelation            Function to calculate and visualise correlation
xDAGanno                Function to generate a subgraph of a direct
                        acyclic graph (DAG) induced by the input
                        annotation data
xDefineEQTL             Function to extract eQTL-gene pairs given a
                        list of SNPs or a customised eQTL mapping data
xDefineHIC              Function to extract promoter capture HiC-gene
                        pairs given a list of SNPs
xDefineNet              Function to define a gene network
xDefineOntology         Function to define ontology and its annotations
xEnrichForest           Function to visualise enrichment results using
                        a forest plot
xEnrichViewer           Function to view enrichment results
xEnricher               Function to conduct enrichment analysis given
                        the input data and the ontology and its
                        annotation
xEnricherGenes          Function to conduct enrichment analysis given a
                        list of genes and the ontology in query
xGGnetwork              Function to visualise an igraph object using
                        ggnetwork
xGR                     Function to create a GRanges object given a
                        list of genomic regions
xGR2nGenes              Function to define nearby genes given a list of
                        genomic regions
xGR2xGeneScores         Function to identify likely modulated seed
                        genes from an input list of genomic regions
                        together with the significance level given the
                        crosslink info
xGR2xGenes              Function to define genes from an input list of
                        genomic regions given the crosslink info
xGRscores               Function to score genomic regions based on the
                        given significance level
xGRsort                 Function to sort by chromosomes/seqnames, start
                        and end coordinates of the intervals.
xGSEAbarplot            Function to visualise GSEA results using a
                        barplot
xGSEAconciser           Function to make GSEA results conciser by
                        removing redundant terms
xGSEAdotplot            Function to visualise GSEA results using dot
                        plot
xGSsimulator            Function to simulate gold standard negatives
                        (GSN) given gold standard positives (GSP) and a
                        gene network
xGeneID2Symbol          Function to convert gene symbols to entrez
                        geneid
xHeatmap                Function to draw heatmap using ggplot2
xLiftOver               Function to lift genomic intervals from one
                        genome build to another.
xMEabf                  Function to conduct colocalisation analysis
                        through Wakefield's Approximate Bayes Factor
                        approach integrating GWAS and eQTL summary data
xMLcaret                Function to integrate predictor matrix in a
                        supervised manner via machine learning
                        algorithms using caret.
xMLcompare              Function to visualise cross-validation
                        performance against tuning parameters
xMLdensity              Function to visualise machine learning results
                        using density plot
xMLdotplot              Function to visualise machine learning results
                        using dot plot
xMLfeatureplot          Function to visualise/assess features used for
                        machine learning
xMLglmnet               Function to integrate predictor matrix in a
                        supervised manner via machine learning
                        algorithm glmnet.
xMLparameters           Function to visualise cross-validation
                        performance against tuning parameters
xMLrandomforest         Function to integrate predictor matrix in a
                        supervised manner via machine learning
                        algorithm random forest.
xMLrename               Function to rename predictors used in machine
                        learning
xMLzoom                 Function to visualise machine learning results
                        using zoom plot
xPieplot                Function to visualise data frame using pie
                        plots
xPier                   Function to do prioritisation through random
                        walk techniques
xPierABF                Function to prioritise genes based on seed
                        eGenes identified through ABF integrating GWAS
                        and eQTL summary data
xPierABFheatmap         Function to visualise ABF evidence using
                        heatmap
xPierAnno               Function to prioritise seed genes only from a
                        list of pNode objects using annotation data
xPierCor                Function to calculate correlation between
                        prioritised genes and user-defined external
                        data
xPierCross              Function to extract priority matrix from a list
                        of dTarget/sTarget objects
xPierEvidence           Function to extract evidence from a list of
                        pNode objects
xPierGRs                Function to prioritise genes given a list of
                        genomic regions
xPierGSEA               Function to prioritise pathways based on GSEA
                        analysis of prioritised genes
xPierGenes              Function to prioritise genes from an input
                        network and the weight info imposed on its
                        nodes
xPierMRS                Function to calculate multi-trait rating score
                        from a list of dTarget/sTarget objects
xPierManhattan          Function to visualise prioritised genes using
                        manhattan plot
xPierMatrix             Function to extract priority or evidence matrix
                        from a list of pNode objects
xPierPathways           Function to prioritise pathways based on
                        enrichment analysis of top prioritised genes
xPierROCR               Function to assess the dTarget performance via
                        ROC and Precision-Recall (PR) analysis
xPierSNPs               Function to prioritise genes given a list of
                        seed SNPs together with the significance level
                        (e.g. GWAS reported p-values)
xPierSNPsAdv            Function to prepare genetic predictors given a
                        list of seed SNPs together with the
                        significance level (e.g. GWAS reported
                        p-values)
xPierSNPsAdvABF         Function to prepare genetic predictors given
                        GWAS summary data with eGenes identified
                        through ABF
xPierSubnet             Function to identify a gene network from top
                        prioritised genes
xPierTrack              Function to visualise a prioritised gene using
                        track plot
xPierTrackAdv           Function to visualise a list of prioritised
                        genes using advanced track plot
xPredictCompare         Function to compare prediction performance
                        results
xPredictROCR            Function to assess the prediction performance
                        via ROC and Precision-Recall (PR) analysis
xRDataLoader            Function to load the package built-in RData
xRWR                    Function to implement Random Walk with Restart
                        (RWR) on the input graph
xSM2DF                  Function to create a data frame (with three
                        columns) from a (sparse) matrix
xSNP2cGenes             Function to define HiC genes given a list of
                        SNPs
xSNP2eGenes             Function to define eQTL genes given a list of
                        SNPs or a customised eQTL mapping data
xSNP2nGenes             Function to define nearby genes given a list of
                        SNPs
xSNPlocations           Function to extract genomic locations given a
                        list of SNPs
xSNPscores              Function to score lead or LD SNPs based on the
                        given significance level
xSparseMatrix           Function to create a sparse matrix for an input
                        file with three columns
xSubneterGenes          Function to identify a subnetwork from an input
                        network and the signficance level imposed on
                        its nodes
xSymbol2GeneID          Function to convert gene symbols to entrez
                        geneid
xVisEvidence            Function to visualise evidence for prioritised
                        genes in a gene network
xVisEvidenceAdv         Function to visualise evidence and priority
                        scores for prioritised genes in a gene network
xVisKernels             Function to visualise distance kernel functions
xVisNet                 Function to visualise a graph object of class
                        "igraph"
