Man pages for xQTLbiolinks
Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

apiAdmin_pingHeartbeat to check GTEx API server connectivity.
apiEbi_pingHeartbeat to check EBI API server connectivity.
dbsnpQueryRangeretrieve snps from dbSNP using coordinate.
EBIquery_allTermEBIquery_allTerm
ebi_study_tissuesdata for vignette
example_Coloc_colocResultAlldata for vignette
example_Coloc_colocResultsigdata for vignette
example_Coloc_gwasDFdata for vignette
example_Coloc_hyprcolocResultAlldata for vignette
example_Coloc_sentinelSNPdata for vignette
example_Coloc_traitsAlldata for vignette
extractGeneInfoextract gene infor of specified genome from...
fetchContentFetch data using url by three methods
fetchContentEbiFetch records from
gencodeGeneInfoAllGrangesGene annotations (chr1-chr22).
gencodeGenetypeGene types in GTEx V8 and V7
is.wholenumberdetermine whether is a whole number:
retrieveLDRetrive SNP pairwise LD from locuscompare database.
sampleNumsamples used in GTEx eQTL analysis.
tissueSiteDetailGTExv7Tissue name and tissue id mapping of GTEx V7.
tissueSiteDetailGTExv8Tissue name and tissue id mapping of GTEx V8.
xQTLanalyze_colocConduct colocalization analysis with trait genes generated...
xQTLanalyze_getSentinelSnpDetect sentinel SNPs in a given summary statistis dataset.
xQTLanalyze_getTraitsIdentify trait genes using sentinel SNPs generated from...
xQTLanalyze_propensityeQTL-specific analysis
xQTLanalyze_TSExpPerform tissue-specific expression analysis for genes.
xQTLdownload_egeneDownload details of eGenes (eQTL Genes) for a specified gene...
xQTLdownload_eqtlDownload significant or unsignificant eQTL associations of a...
xQTLdownload_eqtlAllAssoDownload summary statistics of eQTL of a specified gene,...
xQTLdownload_eqtlAllAssoPosDownload summary statistics of eQTL with genome position.
xQTLdownload_eqtlExpDownload normalized expression of gene for a eQTL pair.
xQTLdownload_eqtlSigDownload significant eQTL associations of a specified tissue...
xQTLdownload_expDownload normalized gene expression at the sample level in a...
xQTLdownload_geneMedExpDownload median expression of all samples for specified genes...
xQTLdownload_sgeneDownload details of sGenes (sQTL Genes) for a specified gene...
xQTLdownload_sqtlExpDownload normalized expression of intron for a sQTL pair.
xQTLdownload_sqtlSigDownload significant sQTL associations of a tissue or across...
xQTLquery_geneQuery basic information (including name, symbol, position and...
xQTLquery_geneAllFetch details of all genes supported in GTEx.
xQTLquery_sampleBySampleIdQuery sample's details with samples' IDs.
xQTLquery_sampleByTissueQuery sample's details with tissue name
xQTLquery_tissueFetch all details of a specified tissue or all tissues
xQTLquery_varIdQuery variant in GTEx with variant ID or dbSNP ID
xQTLquery_varPosQuery varints in GTEx using genome position.
xQTLvisual_eqtlBox plot with jittered points for showing number and...
xQTLvisual_eqtlExpBoxplot of normalized expression among genotypes for eQTL.
xQTLvisual_geneExpTissuesViolin plot of distribution of the gene expression profiles...
xQTLvisual_genesExpDensity plot of expression profiles of the gene
xQTLvisual_locusCombineGenerate a combined figure including locuszoom and...
xQTLvisual_locusCompareDotplot of comparing regional signals between GWAS and xQTL.
xQTLvisual_locusZoomLocuszoom plot for visualizing regional signals relative to...
xQTLvisual_qtlPropensityVisualization of QTL specificity among multiple...
xQTLvisual_sqtlExpBoxplot of normalized expression among genotypes for sQTL.
xQTLbiolinks documentation built on Aug. 27, 2022, 5:05 p.m.