xQTLanno_genomic

annotate all signals in GWAS / QTL dataset by genome location

Enables users-customized data retrieval, processing, analysis, and data visualization of molecular quantitative trait locus and gene expression data from public resources through the application programming interface <https://gtexportal.org/home/api-docs/index.html> of 'GTEx' and <http://www.ebi.ac.uk/eqtl/api> of 'eQTL cagalogue'.

Ruofan Ding

xQTLbiolinks

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

Xudong Zou

Yangmei Qin

Gao Wang

Lei Li

xQTLanno_genomic function

<dl><dt>snpInfo</dt>
<dd>A data.table/data.frame with three columns: chromosome, position, and P-value.</dd>
<dt>p_cutoff</dt>
<dd>Cutoff of p-values of significant variants that will be annotated</dd>
<dt>genomeVersion</dt>
<dd>"hg38" (default) or "hg19". Note: hg19 will be converted to hg38 automatically.</dd></dl>

Arguments

annotate all signals in GWAS / QTL dataset by genome location — xQTLanno_genomic

<dl>

<dt>snpInfo</dt>
<dd>A data.table/data.frame with three columns: chromosome, position, and P-value.</dd>


<dt>p_cutoff</dt>
<dd>Cutoff of p-values of significant variants that will be annotated</dd>


<dt>genomeVersion</dt>
<dd>"hg38" (default) or "hg19". Note: hg19 will be converted to hg38 automatically.</dd>

</dl>

xQTLanno_genomic: annotate all signals in GWAS / QTL dataset by genome location

Description

Usage

Value

Arguments