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

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Documentation for package ‘Pi’ version 2.5.0

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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
xCombineNet Function to combine networks from a list of igraph objects
xContour Function to visualise a numeric matrix as a contour plot
xConverter Function to convert an object between graph classes
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
xEnrichForest Function to visualise enrichment results using a forest plot
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
xLayout Function to define graph node coordinates according to igraph- or sna-style layout
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"