Haploid_regulators      Haploid mutagenesis screens for regulators of
                        protein phenotypes
ImmunoBase              Immune-disease associated variants, regions and
                        genes from ImmunoBase (hg19)
JKscience_TS2A          Table S2A for cis-eQTLs among shared datasets
                        from Benjamin et al. (2014)
aOnto                   Definition for S3 class 'aOnto'
eTerm                   Definition for S3 class 'eTerm'
ls_eTerm                Definition for S3 class 'ls_eTerm'
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
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
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
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
xGR2xGeneScores         Function to identify likely modulated seed
                        genes from an input list of genomic regions
                        together with the significance level given the
                        crosslink info
xGR2xGenes              Function to define genes from an input list of
                        genomic regions given the crosslink info
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
xGeneID2Symbol          Function to convert gene symbols to entrez
                        geneid
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
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.
xMEabf                  Function to conduct colocalisation analysis
                        through Wakefield's Approximate Bayes Factor
                        approach integrating GWAS and eQTL summary data
xOBOcode                Function to create codes annotating nodes in an
                        igraph object
xObjSize                Function to estimate memory allocated for an R
                        variable or a file
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
xSM2DF                  Function to create a data frame (with three
                        columns) from a (sparse) matrix
xSNP2GeneScores         Function to identify likely modulated seed
                        genes given a list of SNPs together with the
                        significance level (e.g. GWAS reported
                        p-values)
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
xSimplifyNet            Function to simplify networks from an igraph
                        object
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
xSubneterGR             Function to identify a gene network from an
                        input network given a list of genomic regions
                        together with the significance level
xSubneterGenes          Function to identify a subnetwork from an input
                        network and the signficance level imposed on
                        its nodes
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"
