# An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

## Documentation for package ‘xQTLbiolinks’ version 1.6.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
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'
xQTLanno_calLambda | calculate genomic control inflation factor for a QTL/GWAS summary statistics dataset.
xQTLanno_chippeak | enrichment analysis for GWAS / QTL signals in functional elements, including enhancer, promoter, CPG, and TFs
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 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
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.
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_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.
xQTL_export | Export expression object to a specified format