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dingruofan edited this page May 26, 2022 · 1 revision

To view documentation for each function, type ?functin name in the R console, like: ?xQTLquery_gene.

xQTLbiolinks current export the following functions:

  1. Query:

    • xQTLquery_gene: query basic information (including gene name, symbol, position and description, etc ) of genes.
    • xQTLquery_geneAll: fetch basic information of all genes.
    • xQTLquery_varId: query variant with variant ID or SNP ID.
    • xQTLquery_varPos: query varints with genome postion.
    • xQTLquery_sampleByTissue: query sample's details with a tissue name.
    • xQTLquery_sampleByTissue: query sample's details with samples' IDs.
    • xQTLquery_tissue: Fetch all detail information of a specified tissue or all tissues.

  2. Download

    • xQTLdownload_eqtl: download significant or unsignificant eQTL data of a tissue or across all tissues.
    • xQTLdownload_eqtlSig: download significant eQTL associations of a tissue or across all tissues.
    • xQTLdownload_eqtlExp: download normalized expression of gene for a eQTL pair.
    • xQTLdownload_eqtlAllAsso: download all tested variant-gene associations.
    • xQTLdownload_egene: download eGenes (eQTL Genes).
    • xQTLdownload_sqtlSig: download significant sQTL associations of a tissue or across all tissues.
    • xQTLdownload_sqtlExp: download normalized expression of intron for a sQTL pair.
    • xQTLdownload_sgene: download sGenes (sQTL Genes).
    • xQTLdownload_exp: download normalized gene expression at the sample level in a specified tissue.
    • xQTLdownload_geneMedExp: download genes' median expression in a tissue or across all tissues.
    • xQTLdownload_ld: download linkage disequilibrium data of the variants associated with this gene.

  3. Ananlysis

    • xQTLanalyze_getSentinelSnp: detect sentinel SNPs in a given GWAS dataset.
    • xQTLanalyze_getTraits: identify trait genes with sentinel SNPs:
    • xQTLanalyze_coloc: conduct colocalization analysis with detected gene.
    • xQTLanalyze_TSExp: perform tissue-specific expression analysis.

  4. Visulization

    • xQTLvisual_eqtl: plot significance of all eQTL associations for a gene across tissues.

    • xQTLvisual_eqtlExp: plot normalized expression among genotypes for eQTL.

    • xQTLvisual_sqtlExp: plot normalized expression among genotypes for sQTL.

    • xQTLvisual_geneCorr: The correlation plot of two genes’ expression.

    • xQTLvisual_genesExp: density plot of specified genes' expression profiles in a specified tissue.

    • xQTLvisual_geneExpTissues: plot distribution of the gene expression among multiple tissues.

    • xQTLvisual_locusZoom: plot locuszoom for showing regional information of the association signal relative to genomic position

    • xQTLvisual_locusCompare: visualize the colocalization of association summary statistics.

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