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

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Documentation for package ‘Pi’ version 1.15.0

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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'
print.cTarget Definition for S3 class 'cTarget'
print.dTarget Definition for S3 class 'dTarget'
print.eGSEA Definition for S3 class 'eGSEA'
print.eTarget Definition for S3 class 'eTarget'
print.pNode Definition for S3 class 'pNode'
print.pPerf Definition for S3 class 'pPerf'
print.sGS Definition for S3 class 'sGS'
print.sTarget Definition for S3 class 'sTarget'
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
xPierGenes Function to prioritise genes from an input network and the weight info imposed on its nodes
xPierGRs Function to prioritise genes given a list of genomic regions
xPierGSEA Function to prioritise pathways based on GSEA analysis of prioritised genes
xPierKEGG Function to visualise prioritised genes in terms of a KEGG pathway
xPierManhattan Function to visualise prioritised genes using manhattan plot
xPierMatrix Function to extract priority or evidence matrix from a list of pNode objects
xPierMRS Function to calculate multi-trait rating score from a list of dTarget/sTarget 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