Man pages for xQTLbiolinks
An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'
| apiAdmin_ping | Heartbeat to check GTEx API server connectivity. |
| apiEbi_ping | Heartbeat to check EBI API server connectivity. |
| dbsnpQueryRange | retrieve snps from dbSNP using coordinate. |
| EBIquery_allTerm | Query supported terms (phenotypes, studies, tissues) in eQTL... |
| ebi_study_tissues | data for vignette |
| example_Coloc_colocResultAll | data for vignette |
| example_Coloc_colocResultsig | data for vignette |
| example_Coloc_gwasDF | data for vignette |
| example_Coloc_hyprcolocResultAll | data for vignette |
| example_Coloc_sentinelSNP | data for vignette |
| example_Coloc_traitsAll | data for vignette |
| extractGeneInfo | Extract gene details from gencodeGeneInfoAllGranges object |
| fetchContent | Fetch data using url by three methods |
| fetchContentEbi | Fetch variant from Ebi |
| gencodeGeneInfoAllGranges | Gene annotations (chr1-chr22). |
| gencodeGenetype | Gene types in GTEx V8 and V7 |
| is.wholenumber | determine whether is a whole number: |
| retrieveLD | Retrieve SNP pairwise LD from locuscompare database |
| retrieveLD_LDproxy | Retrieve SNP pairwise LD from LDlink database |
| sampleNum | samples used in GTEx eQTL analysis. |
| tissueSiteDetailGTExv7 | Tissue name and tissue id mapping of GTEx V7. |
| tissueSiteDetailGTExv8 | Tissue name and tissue id mapping of GTEx V8. |
| xQTLanalyze_coloc | Conduct colocalization analysis with trait genes generated... |
| 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... |
| xQTLanno_calLambda | calculate genomic control inflation factor for a QTL/GWAS... |
| xQTLanno_chippeak | enrichment analysis for GWAS / QTL signals in functional... |
| xQTLanno_genomic | annotate all signals in GWAS / QTL dataset by genome location |
| xQTLdownload_egene | Download eGenes (eQTL Genes) for a specified gene or a tissue |
| xQTLdownload_eqtlAllAsso | Download summary statistics data for eQTLs with a specified... |
| xQTLdownload_eqtlAllAssoPos | Download summary statistics data for eQTLs with genome... |
| xQTLdownload_eqtlExp | Download normalized expression for gene with a variant-gene... |
| xQTLdownload_exp | Download normalized gene expression at the sample level for a... |
| xQTLdownload_geneMedExp | Download median expressions for multiple genes in a specified... |
| xQTLdownload_hqtl | Download summary statistics data of H3K4me1 and H3K27ac... |
| xQTLdownload_hqtlmeta | Download metadata for H3K4me1 and H3K27ac histone QTL (hQTL) |
| xQTLdownload_mQTL | Download summary statistics data of DNA methylation QTL... |
| 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... |
| xQTLdownload_sgene | Download details of sGenes (sQTL Genes) for a specified gene... |
| xQTLdownload_sqtlAllAsso | Download summary statistics data for sQTLs with a specified... |
| xQTLdownload_sqtlExp | Download normalized PSI value of intron for a sQTL pair |
| xQTLdownload_xqtlAllAsso | Download summary statistics of xQTL for a specified gene,... |
| xQTL_export | Export expression object to a specified format |
| xQTLquery_eqtl | Query multi-tissue eQTL metasoft results |
| xQTLquery_eqtlSig | Query significant eQTL associations for a specified tissue or... |
| xQTLquery_gene | Query basic information for genes, including name, symbol,... |
| 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... |
| 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. |
| xQTLvisual_anno | Visualize enrichment of variants derived from... |
| xQTLvisual_coloc | Heatmap plot of the LD-p-value relationship of the eQTL |
| xQTLvisual_eqtl | Box plot with jittered points for showing number and... |
| xQTLvisual_eqtlExp | Boxplot of normalized expression stratified by genotypes for... |
| xQTLvisual_geneExpTissues | Violin plot of distribution of the gene expression profiles... |
| xQTLvisual_genoBox | Boxplot of values stratified by genotypes with customized... |
| xQTLvisual_locusCombine | Generate a combined figure including locusZoom and... |
| xQTLvisual_locusCompare | Dotplot of comparing regional signals between GWAS and xQTL |
| xQTLvisual_locusZoom | Locuszoom plot for visualizing regional signals relative to... |
| xQTLvisual_manhattan | Manhattan plot for a GWAS summary statistics dataset |
| xQTLvisual_PZPlot | Compare P-values reported to P-values calculated from Z... |
| xQTLvisual_qqPlot | Quantile-quantile plot with p-values from GWAS summary... |
| xQTLvisual_sqtl | Box plot with jittered points for showing number and... |
| xQTLvisual_sqtlExp | Boxplot of normalized PSI stratified by genotypes for sQTL. |
