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

## Documentation for package ‘XGR’ version 1.1.5

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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'

## -- X --

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"