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

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Documentation for package ‘Pi’ version 2.12.0

• 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
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"