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

## Documentation for package ‘Pi’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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
xPCHiCplot | Function to visualise promoter capture HiC data using different network layouts
xPieplot | Function to visualise data frame using pie plots
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
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
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
xVisEvidenceAdv | Function to visualise evidence and priority scores for prioritised genes in a gene network