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_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.