Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

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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.