Exploring Genomic Relations at the Gene and SNP Level Through Enrichment, Similarity and Network Analysis


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Documentation for package ‘XGR’ version 1.0.1

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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)
xCircos Function to visualise a network as a circos plot
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
xDAGsim Function to calculate pair-wise semantic similarity between input terms based on a direct acyclic graph (DAG) with annotated data
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
xEnrichViewer Function to view enrichment results
xFunArgs Function to assign (and evaluate) arguments with default values for a given function
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
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
xSNPscores Function to score input SNPs from the given significance level
xSocialiser Function to calculate pair-wise semantic similarity given the input data and the ontology and its annotation
xSocialiserGenes Function to calculate pair-wise semantic similarity given a list of genes and the ontology in query
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
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)
xVisKernels Function to visualise distance kernel functions
xVisNet Function to visualise a graph object of class "igraph"