Function reference • xQTLbiolinks

Data retrieval
`xQTLquery_eqtl()`	Query multi-tissue eQTL metasoft results
`xQTLquery_eqtlSig()`	Query significant eQTL associations for a specified tissue or multiple tissues.
`xQTLquery_gene()`	Query basic information for genes, including name, symbol, position and description
`xQTLquery_geneAll()`	Query all genes supported in GTEx
`xQTLquery_sampleBySampleId()`	Query details of samples with GTEx IDs
`xQTLquery_sampleByTissue()`	Query details of samples by tissue name
`xQTLquery_sc()`	Query significant sc-eQTLs for a specified gene
`xQTLquery_scInfo()`	Query metadata of sc-eQTLs
`xQTLquery_sqtlSig()`	Query significant sQTL associations for a tissue or multple tissues
`xQTLquery_tissue()`	Query details for a specified tissue
`xQTLquery_varId()`	Query variant with variant ID or dbSNP ID
`xQTLquery_varPos()`	Query variants using genome position.
`xQTLdownload_egene()`	Download eGenes (eQTL Genes) for a specified gene or a tissue
`xQTLdownload_eqtlAllAsso()`	Download summary statistics data for eQTLs with a specified gene, variant, tissue or study
`xQTLdownload_eqtlAllAssoPos()`	Download summary statistics data for eQTLs with genome positions.
`xQTLdownload_eqtlExp()`	Download normalized expression for gene with a variant-gene pair
`xQTLdownload_exp()`	Download normalized gene expression at the sample level for a specified tissue.
`xQTLdownload_geneMedExp()`	Download median expressions for multiple genes in a specified tissue
`xQTLdownload_hqtl()`	Download summary statistics data of H3K4me1 and H3K27ac histone QTL (hQTL) using a specified location
`xQTLdownload_hqtlmeta()`	Download metadata for H3K4me1 and H3K27ac histone QTL (hQTL)
`xQTLdownload_mQTL()`	Download summary statistics data of DNA methylation QTL (mQTL) using CpG ID
`xQTLdownload_mqtlmeta()`	Download metadata of DNA methylation QTL (mQTL)
`xQTLdownload_sc()`	Download all sc-eQTL associations for a specified gene
`xQTLdownload_scSig()`	Download significant sc-eQTL associations for a specified gene
`xQTLdownload_sgene()`	Download details of sGenes (sQTL Genes) for a specified gene or a tissue.
`xQTLdownload_sqtlAllAsso()`	Download summary statistics data for sQTLs with a specified gene or a tissue
`xQTLdownload_sqtlExp()`	Download normalized PSI value of intron for a sQTL pair
`xQTLdownload_xqtlAllAsso()`	Download summary statistics of xQTL for a specified gene, default:3'aQTL
`EBIquery_allTerm()`	Query supported terms (phenotypes, studies, tissues) in eQTL catalogue
`extractGeneInfo()`	Extract gene details from gencodeGeneInfoAllGranges object
`retrieveLD()`	Retrieve SNP pairwise LD from locuscompare database
`retrieveLD_LDproxy()`	Retrieve SNP pairwise LD from LDlink database
Pre-processing
`xQTLanno_calLambda()`	Calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset
`xQTLanno_chippeak()`	Annotate GWAS / QTL signals using bed4 format table object that provided by user
`xQTLanno_genomic()`	Genomic annotation of significant signals from GWAS / QTL
`xQTL_export()`	Export expression object to a specified format
Analyze
`xQTLanalyze_coloc()`	Conduct colocalization analysis with trait genes generated from `xQTLanalyze_getTraits`
`xQTLanalyze_coloc_diy()`	Conduct colocalization analysis with customized QTL data
`xQTLanalyze_getSentinelSnp()`	Detect sentinel SNPs for GWAS using summary statistics data
`xQTLanalyze_getTraits()`	Identify trait genes using sentinel SNPs generated from `xQTLanalyze_getSentinelSnp`
Visualize
`xQTLvisual_anno()`	Visualize enrichment of variants derived from `xQTLanno_genomic`
`xQTLvisual_coloc()`	Heatmap plot of the LD-p-value relationship of the eQTL
`xQTLvisual_eqtl()`	Box plot with jittered points for showing number and significance of eQTL associations
`xQTLvisual_eqtlExp()`	Boxplot of normalized expression stratified by genotypes for eQTL.
`xQTLvisual_geneExpTissues()`	Violin plot of distribution of the gene expression profiles among multiple tissues.
`xQTLvisual_genesExp()`	Density plot of expression profiles for multiple genes
`xQTLvisual_genoBox()`	Boxplot of values stratified by genotypes with customized data
`xQTLvisual_locusCombine()`	Generate a combined figure including locusZoom and locuscompare plot
`xQTLvisual_locusCompare()`	Dotplot of comparing regional signals between GWAS and xQTL
`xQTLvisual_locusZoom()`	Locuszoom plot for visualizing regional signals relative to genomic position with summary statistics data
`xQTLvisual_manhattan()`	Manhattan plot for a GWAS summary statistics dataset
`xQTLvisual_PZPlot()`	Compare P-values reported to P-values calculated from Z statistics derived from the reported beta and standard error.
`xQTLvisual_qqPlot()`	Quantile-quantile plot with p-values from GWAS summary statistics data
`xQTLvisual_sqtl()`	Box plot with jittered points for showing number and significance of sQTL associations
`xQTLvisual_sqtlExp()`	Boxplot of normalized PSI stratified by genotypes for sQTL.

Reference

Data retrieval

Pre-processing

Analyze

Visualize