Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'


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Documentation for package ‘xQTLbiolinks’ version 1.4.2

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EBIquery_allTerm Query supported terms (phenotypes, studies, tissues) in eQTL catalogue
extractGeneInfo Extract gene infor of specified genome from gencodeGeneInfoAllGranges
retrieveLD Retrive SNP pairwise LD from locuscompare database.
retrieveLD_LDproxy Retrive SNP pairwise LD from LDlink database
xQTLanalyze_coloc Conduct colocalization analysis with trait genes generated from 'xQTLanalyze_getTraits'
xQTLanalyze_coloc_diy conduct colocalization analysis with customized xQTL data
xQTLanalyze_getSentinelSnp Detect sentinel SNPs in a given summary statistis dataset.
xQTLanalyze_getTraits Identify trait genes using sentinel SNPs generated from 'xQTLanalyze_getSentinelSnp'
xQTLanno_calLambda calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset.
xQTLanno_enrich enrichment analysis for GWAS / QTL signals in functional elements, including enhancer, promoter, CPG, and TFs
xQTLanno_genomic annotate all signals in GWAS / QTL dataset by genome location
xQTLdownload_egene Download details of eGenes (eQTL Genes) for a specified gene or a tissue.
xQTLdownload_eqtlAllAsso Download summary statistics of eQTL of a specified gene, variant, tissue or study.
xQTLdownload_eqtlAllAssoPos Download summary statistics of eQTL with genome position.
xQTLdownload_eqtlExp Download normalized expression of gene for a eQTL pair.
xQTLdownload_exp Download normalized gene expression at the sample level in a specified tissue.
xQTLdownload_geneMedExp Download median expression of all samples for specified genes across tissues.
xQTLdownload_sgene Download details of sGenes (sQTL Genes) for a specified gene or a tissue.
xQTLdownload_sqtlAllAsso download summary statistics of sQTL of a specified gene in GTEx v8.
xQTLdownload_sqtlExp Download normalized expression of intron for a sQTL pair.
xQTLdownload_xqtlAllAsso Download summary statistics of xQTL of a specified gene in GTEx v8, default:3'aQTL
xQTLquery_eqtl query multi-tissue eQTL metasoft results
xQTLquery_eqtlSig Download significant eQTL associations of a specified tissue or across all tissues.
xQTLquery_gene Query basic information (including name, symbol, position and description, etc. ) of genes.
xQTLquery_geneAll Fetch details of all genes supported in GTEx.
xQTLquery_sampleBySampleId Query sample's details with samples' IDs.
xQTLquery_sampleByTissue Query sample's details with tissue name
xQTLquery_sqtlSig Download significant sQTL associations of a tissue or across all tissues
xQTLquery_tissue Fetch all details of a specified tissue or all tissues
xQTLquery_varId Query variant in GTEx with variant ID or dbSNP ID
xQTLquery_varPos Query varints in GTEx using genome position.
xQTLvisual_anno Visualizing annotated variants
xQTLvisual_coloc heatmap of LD-p-value of the QTL
xQTLvisual_enrich Visualizing enriched variants
xQTLvisual_eqtl Box plot with jittered points for showing number and significance of eQTL associations
xQTLvisual_eqtlExp Boxplot of normalized expression among genotypes for eQTL.
xQTLvisual_geneExpTissues Violin plot of distribution of the gene expression profiles among multiple tissues.
xQTLvisual_genesExp Density plot of expression profiles of the gene
xQTLvisual_locusCombine Generate a combined figure including locuszoom and locuscompare plot object.
xQTLvisual_locusCompare Dotplot of comparing regional signals between GWAS and xQTL.
xQTLvisual_locusZoom Locuszoom plot for visualizing regional signals relative to genomic position with a file of summary statistics
xQTLvisual_manhattan Advanced CM plot of 11
xQTLvisual_PZPlot Compare P-values reported in the association result file to P-values calculated from Z statistics derived from the reported beta and standard error.
xQTLvisual_qqPlot plot quantile-quantile plot with pvalue
xQTLvisual_sqtl Box plot with jittered points for showing number and significance of sQTL associations
xQTLvisual_sqtlExp Boxplot of normalized expression among genotypes for sQTL.