# Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

## Documentation for package ‘xQTLbiolinks’ version 1.2.2

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

## Help Pages

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 | EBIquery_allTerm
extractGeneInfo | extract gene infor of specified genome from gencodeGeneInfoAllGranges
fetchContent | Fetch data using url by three methods
fetchContentEbi | Fetch records from
is.wholenumber | determine whether is a whole number:
retrieveLD | Retrive SNP pairwise LD from locuscompare database.
xQTLanalyze_coloc | Conduct colocalization analysis with trait genes generated from 'xQTLanalyze_getTraits'
xQTLanalyze_getSentinelSnp | Detect sentinel SNPs in a given summary statistis dataset.
xQTLanalyze_getTraits | Identify trait genes using sentinel SNPs generated from 'xQTLanalyze_getSentinelSnp'
xQTLanalyze_propensity | eQTL-specific analysis
xQTLanalyze_TSExp | Perform tissue-specific expression analysis for genes.
xQTLdownload_egene | Download details of eGenes (eQTL Genes) for a specified gene or a tissue.
xQTLdownload_eqtl | Download significant or unsignificant eQTL associations of a tissue or across all tissues
xQTLdownload_eqtlAllAsso | Download summary statistics of eQTL of a specified gene, variant, tissue or study.
xQTLdownload_eqtlAllAssoPos | Download summary statistics of eQTL with genome position.
xQTLdownload_eqtlExp | Download normalized expression of gene for a eQTL pair.
xQTLdownload_eqtlSig | Download significant eQTL associations of a specified tissue or across all tissues.
xQTLdownload_exp | Download normalized gene expression at the sample level in a specified tissue.
xQTLdownload_geneMedExp | Download median expression of all samples for specified genes across tissues.
xQTLdownload_sgene | Download details of sGenes (sQTL Genes) for a specified gene or a tissue.
xQTLdownload_sqtlExp | Download normalized expression of intron for a sQTL pair.
xQTLdownload_sqtlSig | Download significant sQTL associations of a tissue or across all tissues
xQTLquery_gene | Query basic information (including name, symbol, position and description, etc. ) of genes.
xQTLquery_geneAll | Fetch details of all genes supported in GTEx.
xQTLquery_sampleBySampleId | Query sample's details with samples' IDs.
xQTLquery_sampleByTissue | Query sample's details with tissue name
xQTLquery_tissue | Fetch all details of a specified tissue or all tissues
xQTLquery_varId | Query variant in GTEx with variant ID or dbSNP ID
xQTLquery_varPos | Query varints in GTEx using genome position.
xQTLvisual_eqtl | Box plot with jittered points for showing number and significance of eQTL associations
xQTLvisual_eqtlExp | Boxplot of normalized expression among genotypes for eQTL.
xQTLvisual_geneExpTissues | Violin plot of distribution of the gene expression profiles among multiple tissues.
xQTLvisual_genesExp | Density plot of expression profiles of the gene
xQTLvisual_locusCombine | Generate a combined figure including locuszoom and locuscompare plot object.
xQTLvisual_locusCompare | Dotplot of comparing regional signals between GWAS and xQTL.
xQTLvisual_locusZoom | Locuszoom plot for visualizing regional signals relative to genomic position with a file of summary statistics
xQTLvisual_qtlPropensity | Visualization of QTL specificity among multiple cells/tissues.
xQTLvisual_sqtlExp | Boxplot of normalized expression among genotypes for sQTL.