cTarget                 Definition for S3 class 'cTarget'
dTarget                 Definition for S3 class 'dTarget'
eGSEA                   Definition for S3 class 'eGSEA'
eTarget                 Definition for S3 class 'eTarget'
pNode                   Definition for S3 class 'pNode'
pPerf                   Definition for S3 class 'pPerf'
sGS                     Definition for S3 class 'sGS'
sTarget                 Definition for S3 class 'sTarget'
xContour                Function to visualise a numeric matrix as a
                        contour plot
xCorrelation            Function to calculate and visualise correlation
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
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
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
xPierKEGG               Function to visualise prioritised genes in
                        terms of a KEGG pathway
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
xPierSNPsConsensus      Function to resolve relative importance of
                        distance weight and eQTL weight priorising
                        consensus gene ranks given a list of seed SNPs
                        together with the significance level (e.g. GWAS
                        reported p-values)
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
xRWR                    Function to implement Random Walk with Restart
                        (RWR) on the input graph
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
