| xAddCoords |
Function to add coordinates into a graph according to a node attribute |
| xAggregate |
Function to aggregate data respecting number of features |
| xAuxEmbed |
Function to encode a file as a base64 string for embedding |
| xAuxFunArgs |
Function to assign (and evaluate) arguments with default values for a given function |
| xAuxRd2HTML |
Function to convert Rd files to HTML files |
| xAuxRdWrap |
Function to wrap texts from Rd files |
| 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 |
| xConverter |
Function to convert an object between graph classes |
| xCtree |
Function to draw a tree-like circular plot |
| xDAGanno |
Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data |
| xDAGpropagate |
Function to generate a subgraph of a direct acyclic graph (DAG) propagaged by the input annotation data |
| xDAGsim |
Function to calculate pair-wise semantic similarity between input terms based on a direct acyclic graph (DAG) with annotated data |
| xDefineEQTL |
Function to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data |
| xDefineGenomicAnno |
Function to define genomic annotations |
| 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 |
| xEnrichBarplot |
Function to visualise enrichment results using a barplot |
| xEnrichChord |
Function to visualise enrichment results using a chord plot |
| xEnrichCompare |
Function to compare enrichment results using side-by-side barplots |
| xEnrichConciser |
Function to make enrichment results conciser by removing redundant terms |
| xEnrichCtree |
Function to visualise enrichment results using a tree-like circular plot |
| xEnrichD3 |
Function to visualise enrichment results using a D3 plot |
| xEnrichDAGplot |
Function to visualise enrichment results using a direct acyclic graph (DAG) |
| xEnrichDAGplotAdv |
Function to visualise comparative enrichment results using a direct acyclic graph (DAG) |
| xEnrichDotplot |
Function to visualise enrichment results using dot-like plot |
| 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 |
| xEnricherGenesAdv |
Function to conduct enrichment analysis given a list of gene sets and a list of ontologies |
| xEnricherSNPs |
Function to conduct enrichment analysis given a list of SNPs and the ontology in query |
| xEnricherYours |
Function to conduct enrichment analysis given YOUR own input data |
| xEnrichForest |
Function to visualise enrichment results using a forest plot |
| xEnrichGGraph |
Function to visualise enrichment results using a ggraph-like lauout |
| xEnrichHeatmap |
Function to visualise enrichment results using heatmap |
| xEnrichLadder |
Function to visualise enrichment results using ladder-like plot |
| xEnrichMatrix |
Function to compare enrichment results using matrix plots |
| xEnrichNetplot |
Function to visualise enrichment results using different network layouts |
| xEnrichRadial |
Function to visualise enrichment results using radial-like plot |
| xEnrichTreemap |
Function to visualise enrichment results using a treemap |
| xEnrichViewer |
Function to view enrichment results |
| xGeneID2Symbol |
Function to convert gene symbols to entrez geneid |
| xGGnetwork |
Function to visualise an igraph object using ggnetwork |
| xGGraph |
Function to visualise an igraph object using ggraph |
| xGR |
Function to create a GRanges object given a list of genomic regions |
| xGR2GeneScores |
Function to identify likely modulated seed genes given a list of genomic regions together with the significance level |
| xGR2nGenes |
Function to define nearby genes given a list of genomic regions |
| xGR2xGeneAnno |
Function to conduct region-based enrichment analysis via crosslinked genes |
| xGR2xGeneAnnoAdv |
Function to conduct region-based enrichment analysis via crosslinked genes given a list of genomic region sets and a list of ontologies |
| 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 |
| xGraphML |
Function to generate a graphml file from a graph object of class "igraph" |
| xGraphML2AA |
Function to generate a graphml file from a pathway upon query |
| xGRcse |
Function to create a vector storing genomic regions |
| xGRsampling |
Function to generate random samples for data genomic regions from background genomic regions |
| xGRscores |
Function to score genomic regions based on the given significance level |
| xGRsep |
Function to obtain separator index. |
| xGRsort |
Function to sort by chromosomes/seqnames, start and end coordinates of the intervals. |
| xGRviaGeneAnno |
Function to conduct region-based enrichment analysis using nearby gene annotations |
| xGRviaGeneAnnoAdv |
Function to conduct region-based enrichment analysis given a list of genomic region sets and a list of ontologies |
| xGRviaGenomicAnno |
Function to conduct region-based enrichment analysis using genomic annotations via binomial test |
| xGRviaGenomicAnnoAdv |
Function to conduct region-based enrichment analysis using genomic annotations via sampling |
| xHeatmap |
Function to draw heatmap using ggplot2 |
| xHeatmapAdv |
Function to draw heatmap together with sidebars on rows 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. |
| xMarkNet |
Function to mark a network within another network |
| xMEabf |
Function to conduct colocalisation analysis through Wakefield's Approximate Bayes Factor approach integrating GWAS and eQTL summary data |
| xObjSize |
Function to estimate memory allocated for an R variable or a file |
| xOBOcode |
Function to create codes annotating nodes in an igraph object |
| xPieplot |
Function to visualise data frame using pie plots |
| xRDataLoader |
Function to load the package built-in RData |
| xReport |
Function to generate a html-formatted report |
| xSimplifyNet |
Function to simplify networks from an igraph object |
| 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 |
| xSNP2GeneScores |
Function to identify likely modulated seed genes given a list of SNPs together with the significance level (e.g. GWAS reported p-values) |
| 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 |
| xSocialiser |
Function to calculate pair-wise semantic similarity given the input data and the ontology and its annotation |
| xSocialiserDAGplot |
Function to draw DAG plot for visualising terms used to annotate an input SNP or gene |
| xSocialiserDAGplotAdv |
Function to draw DAG plot for comparing two sets of terms used to annotate two SNPs or genes in query |
| xSocialiserGenes |
Function to calculate pair-wise semantic similarity given a list of genes and the ontology in query |
| xSocialiserNetplot |
Function to visualise terms used to annotate an input SNP or gene using different network layouts |
| xSocialiserSNPs |
Function to calculate pair-wise semantic similarity given a list of SNPs and the ontology in query |
| 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 |
| xSubneterGenesAdv |
Function to iteratively identify subnetworks from an input network and the signficance level imposed on its nodes |
| xSubneterGenesMST |
Function to identify a minimum spanning tree for subnetworks |
| xSubneterGR |
Function to identify a gene network from an input network given a list of genomic regions together with the significance level |
| xSubneterSNPs |
Function to identify a gene network from an input network given a list of seed SNPs together with the significance level (e.g. GWAS reported p-values) |
| xSymbol2GeneID |
Function to convert gene symbols to entrez geneid |
| xVisKernels |
Function to visualise distance kernel functions |
| xVisNet |
Function to visualise a graph object of class "igraph" |