Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis


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Documentation for package ‘XGR’ version 1.1.6

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A E H I J L P X

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aOnto Definition for S3 class 'aOnto'

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eTerm Definition for S3 class 'eTerm'

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Haploid_regulators Haploid mutagenesis screens for regulators of protein phenotypes

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ImmunoBase Immune-disease associated variants, regions and genes from ImmunoBase (hg19)

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JKscience_TS2A Table S2A for cis-eQTLs among shared datasets from Benjamin et al. (2014)

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ls_eTerm Definition for S3 class 'ls_eTerm'

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print.aOnto Definition for S3 class 'aOnto'
print.eTerm Definition for S3 class 'eTerm'
print.ls_eTerm Definition for S3 class 'ls_eTerm'

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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.
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
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"