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

## Documentation for package ‘XGR’ version 1.0.10

- DESCRIPTION file.
- Package NEWS.

## Help Pages

eTerm | Definition for S3 class 'eTerm'
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)
print.eTerm | Definition for S3 class 'eTerm'
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
xConverter | Function to convert an object between graph classes
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
xDefineNet | Function to define a gene network
xEnrichBarplot | Function to visualise enrichment results using a barplot
xEnrichCompare | Function to compare enrichment results using side-by-side barplots
xEnrichConciser | Function to make enrichment results conciser by removing redundant terms
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)
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
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
xEnrichNetplot | Function to visualise enrichment results using different network layouts
xEnrichViewer | Function to view enrichment results
xFunArgs | Function to assign (and evaluate) arguments with default values for a given function
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
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
xGRviaGeneAnno | Function to conduct region-based enrichment analysis using nearby gene annotations
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
xLiftOver | Function to lift genomic intervals from one genome build to another.
xRd2HTML | Function to convert Rd files to HTML files
xRDataLoader | Function to load the package built-in RData
xRdWrap | Function to wrap texts from Rd files
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)
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
xVisInterp | Function to visualise interpolated irregular data
xVisKernels | Function to visualise distance kernel functions
xVisNet | Function to visualise a graph object of class "igraph"