Function reference • xQTLbiolinks

Query
`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_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.
`EBIquery_allTerm()`	EBIquery_allTerm
`extractGeneInfo()`	extract gene infor of specified genome from gencodeGeneInfoAllGranges
Download
`xQTLdownload_egene()`	Download details of eGenes (eQTL Genes) for a specified gene or a tissue.
`xQTLdownload_eqtl()`	Download significant or unsignificant eQTL associations of a tissue or across all tissues
`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_eqtlSig()`	Download significant eQTL associations of a specified tissue or across all tissues.
`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_sqtlExp()`	Download normalized expression of intron for a sQTL pair.
`xQTLdownload_sqtlSig()`	Download significant sQTL associations of a tissue or across all tissues
`retrieveLD()`	Retrive SNP pairwise LD from locuscompare database.
`retrieveLD_LDproxy()`	Retrive SNP pairwise LD from LDlink database
Visualize
`xQTLvisual_anno()`	Visualizing annotated variants
`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_PNPlot()`	P-N plot
`xQTLvisual_qqPlot()`	plot quantile-quantile plot with pvalue
`xQTLvisual_qtlPropensity()`	Visualization of QTL specificity among multiple cells/tissues.
`xQTLvisual_sqtlExp()`	Boxplot of normalized expression among genotypes for sQTL.
Analyze
`xQTLanalyze_anno()`	annotate variants with genome positon
`xQTLanalyze_calLambda()`	calculate genomic control inflation factor
`xQTLanalyze_coloc()`	Conduct colocalization analysis with trait genes generated from `xQTLanalyze_getTraits`
`xQTLanalyze_coloc_diy()`	conduct colocalization analysis with customized QTL data
`xQTLanalyze_enrich()`	variant enrichment analysis
`xQTLanalyze_getSentinelSnp()`	Detect sentinel SNPs in a given summary statistis dataset.
`xQTLanalyze_getTraits()`	Identify trait genes using sentinel SNPs generated from `xQTLanalyze_getSentinelSnp`
`xQTLanalyze_propensity()`	eQTL-specific analysis

Reference

Query

Download

Visualize

Analyze