xContour                Function to visualise a numeric matrix as a
                        contour plot
xGSsimulator            Function to simulate gold standard negatives
                        (GSN) given gold standard positives (GSP) and a
                        gene network
xMLdensity              Function to visualise machine learning results
                        using density plot
xMLdotplot              Function to visualise machine learning results
                        using dot plot
xMLrandomforest         Function to integrate predictor matrix in a
                        supervised manner via machine learning
                        algorithm random forest.
xPCHiCplot              Function to visualise promoter capture HiC data
                        using different network layouts
xPier                   Function to do prioritisation through random
                        walk techniques
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 matrix from a list
                        of pNode objects
xPierPathways           Function to prioritise pathways based on
                        enrichment analysis of top prioritised genes
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 prioritised genes using
                        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
