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

## Documentation for package ‘Pi’ version 2.0.0

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

## Help Pages

A C D E G I L P S X

## -- A --

aOnto | Definition for S3 class 'aOnto'

## -- C --

cTarget | Definition for S3 class 'cTarget'

## -- D --

dTarget | Definition for S3 class 'dTarget'

## -- E --

EG | Definition for S3 class 'EG'
eGSEA | Definition for S3 class 'eGSEA'
eTarget | Definition for S3 class 'eTarget'
eTerm | Definition for S3 class 'eTerm'

## -- G --

GS | Definition for S3 class 'GS'

## -- I --

iSubg | Definition for S3 class 'iSubg'

## -- L --

ls_eTerm | Definition for S3 class 'ls_eTerm'

## -- P --

pNode | Definition for S3 class 'pNode'
pPerf | Definition for S3 class 'pPerf'
print.aOnto | Definition for S3 class 'aOnto'
print.cTarget | Definition for S3 class 'cTarget'
print.dTarget | Definition for S3 class 'dTarget'
print.EG | Definition for S3 class 'EG'
print.eGSEA | Definition for S3 class 'eGSEA'
print.eTarget | Definition for S3 class 'eTarget'
print.eTerm | Definition for S3 class 'eTerm'
print.GS | Definition for S3 class 'GS'
print.iSubg | Definition for S3 class 'iSubg'
print.ls_eTerm | Definition for S3 class 'ls_eTerm'
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'

## -- S --

sGS | Definition for S3 class 'sGS'
sTarget | Definition for S3 class 'sTarget'

## -- X --

xAggregate | Function to aggregate data respecting number of features
xCheckParallel | Function to check whether parallel computing should be used and how
xCircos | Function to visualise a network as a circos plot
xColormap | Function to define a colormap
xContour | Function to visualise a numeric matrix as a contour plot
xCorrelation | Function to calculate and visualise correlation
xDAGanno | Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data
xDefineEQTL | Function to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data
xDefineHIC | Function to extract promoter capture HiC-gene pairs given a list of SNPs
xDefineNet | Function to define a gene network
xDefineOntology | Function to define ontology and its annotations
xEnricher | Function to conduct enrichment analysis given the input data and the ontology and its annotation
xEnricherGenes | Function to conduct enrichment analysis given a list of genes and the ontology in query
xEnrichViewer | Function to view enrichment results
xGeneID2Symbol | Function to convert gene symbols to entrez geneid
xGGnetwork | Function to visualise an igraph object using ggnetwork
xGR | Function to create a GRanges object given a list of genomic regions
xGR2nGenes | Function to define nearby genes given a list of genomic regions
xGR2xGenes | Function to define genes from an input list of genomic regions given the crosslink info
xGR2xGeneScores | Function to identify likely modulated seed genes from an input list of genomic regions together with the significance level given the crosslink info
xGRscores | Function to score genomic regions based on the given significance level
xGRsort | Function to sort by chromosomes/seqnames, start and end coordinates of the intervals.
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
xHeatmap | Function to draw heatmap using ggplot2
xLiftOver | Function to lift genomic intervals from one genome build to another.
xMEabf | Function to conduct colocalisation analysis through Wakefield's Approximate Bayes Factor approach integrating GWAS and eQTL summary data
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
xPieplot | Function to visualise data frame using pie plots
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
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
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
xRDataLoader | Function to load the package built-in RData
xRWR | Function to implement Random Walk with Restart (RWR) on the input graph
xSM2DF | Function to create a data frame (with three columns) from a (sparse) matrix
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
xSNP2nGenes | Function to define nearby genes given a list of SNPs
xSNPlocations | Function to extract genomic locations given a list of SNPs
xSNPscores | Function to score lead or LD SNPs based on the given significance level
xSparseMatrix | Function to create a sparse matrix for an input file with three columns
xSubneterGenes | Function to identify a subnetwork from an input network and the signficance level imposed on its nodes
xSymbol2GeneID | Function to convert gene symbols to entrez geneid
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
xVisKernels | Function to visualise distance kernel functions
xVisNet | Function to visualise a graph object of class "igraph"