| 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" |