Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level

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Documentation for package ‘Pi’ version 1.2.1

Help Pages

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