| aOnto | Definition for S3 class 'aOnto' |
| cTarget | Definition for S3 class 'cTarget' |
| dTarget | Definition for S3 class 'dTarget' |
| EG | Definition for S3 class 'EG' |
| eGSEA | Definition for S3 class 'eGSEA' |
| eTarget | Definition for S3 class 'eTarget' |
| eTerm | Definition for S3 class 'eTerm' |
| GS | Definition for S3 class 'GS' |
| iSubg | Definition for S3 class 'iSubg' |
| ls_eTerm | Definition for S3 class 'ls_eTerm' |
| pNode | Definition for S3 class 'pNode' |
| pPerf | Definition for S3 class 'pPerf' |
| sGS | Definition for S3 class 'sGS' |
| sTarget | Definition for S3 class 'sTarget' |
| xAggregate | Function to aggregate data respecting number of features |
| xCheckParallel | Function to check whether parallel computing should be used... |
| 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... |
| xDefineEQTL | Function to extract eQTL-gene pairs given a list of SNPs or a... |
| xDefineHIC | Function to extract promoter capture HiC-gene pairs given a... |
| 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... |
| xEnricherGenes | Function to conduct enrichment analysis given a list of genes... |
| 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... |
| xGR2nGenes | Function to define nearby genes given a list of genomic... |
| xGR2xGenes | Function to define genes from an input list of genomic... |
| xGR2xGeneScores | Function to identify likely modulated seed genes from an... |
| xGRscores | Function to score genomic regions based on the given... |
| xGRsort | Function to sort by chromosomes/seqnames, start and end... |
| xGSEAbarplot | Function to visualise GSEA results using a barplot |
| xGSEAconciser | Function to make GSEA results conciser by removing redundant... |
| xGSEAdotplot | Function to visualise GSEA results using dot plot |
| xGSsimulator | Function to simulate gold standard negatives (GSN) given gold... |
| xHeatmap | Function to draw heatmap using ggplot2 |
| xLayout | Function to define graph node coordinates according to... |
| xLiftOver | Function to lift genomic intervals from one genome build to... |
| xMEabf | Function to conduct colocalisation analysis through... |
| xMLcaret | Function to integrate predictor matrix in a supervised manner... |
| xMLcompare | Function to visualise cross-validation performance against... |
| xMLdensity | Function to visualise machine learning results using density... |
| xMLdotplot | Function to visualise machine learning results using dot plot |
| xMLfeatureplot | Function to visualise/assess features used for machine... |
| xMLglmnet | Function to integrate predictor matrix in a supervised manner... |
| xMLparameters | Function to visualise cross-validation performance against... |
| xMLrandomforest | Function to integrate predictor matrix in a supervised manner... |
| xMLrename | Function to rename predictors used in machine learning |
| xMLzoom | Function to visualise machine learning results using zoom... |
| 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... |
| xPierABFheatmap | Function to visualise ABF evidence using heatmap |
| xPierAnno | Function to prioritise seed genes only from a list of pNode... |
| xPierCor | Function to calculate correlation between prioritised genes... |
| xPierCross | Function to extract priority matrix from a list of... |
| xPierEvidence | Function to extract evidence from a list of pNode objects |
| xPierGenes | Function to prioritise genes from an input network and the... |
| xPierGRs | Function to prioritise genes given a list of genomic regions |
| xPierGSEA | Function to prioritise pathways based on GSEA analysis of... |
| xPierManhattan | Function to visualise prioritised genes using manhattan plot |
| xPierMatrix | Function to extract priority or evidence matrix from a list... |
| xPierMRS | Function to calculate multi-trait rating score from a list of... |
| xPierPathways | Function to prioritise pathways based on enrichment analysis... |
| xPierROCR | Function to assess the dTarget performance via ROC and... |
| xPierSNPs | Function to prioritise genes given a list of seed SNPs... |
| xPierSNPsAdv | Function to prepare genetic predictors given a list of seed... |
| xPierSNPsAdvABF | Function to prepare genetic predictors given GWAS summary... |
| xPierSubnet | Function to identify a gene network from top prioritised... |
| xPierTrack | Function to visualise a prioritised gene using track plot |
| xPierTrackAdv | Function to visualise a list of prioritised genes using... |
| xPredictCompare | Function to compare prediction performance results |
| xPredictROCR | Function to assess the prediction performance via ROC and... |
| xRDataLoader | Function to load the package built-in RData |
| xRWR | Function to implement Random Walk with Restart (RWR) on the... |
| xSM2DF | Function to create a data frame (with three columns) from a... |
| xSNP2cGenes | Function to define HiC genes given a list of SNPs |
| xSNP2eGenes | Function to define eQTL genes given a list of SNPs or a... |
| 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... |
| xSparseMatrix | Function to create a sparse matrix for an input file with... |
| xSubneterGenes | Function to identify a subnetwork from an input network and... |
| xSymbol2GeneID | Function to convert gene symbols to entrez geneid |
| xVisEvidence | Function to visualise evidence for prioritised genes in a... |
| xVisEvidenceAdv | Function to visualise evidence and priority scores for... |
| xVisKernels | Function to visualise distance kernel functions |
| xVisNet | Function to visualise a graph object of class "igraph" |
