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
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 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.
xMLzoom                 Function to visualise machine learning results
                        using zoom plot
xPCHiCplot              Function to visualise promoter capture HiC data
                        using different network layouts
xPier                   Function to do prioritisation through random
                        walk techniques
xPierAnno               Function to prioritise seed genes only from a
                        list of pNode objects using annotation 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
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
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)
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
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
xSNPeqtl                Function to extract eQTL-gene pairs given a
                        list of SNPs or a customised eQTL mapping data
xSNPhic                 Function to extract promoter capture HiC-gene
                        pairs given a list of SNPs
xVisEvidence            Function to visualise evidence for prioritised
                        genes in a gene network
