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" |