link_eqtl: Obtain GTEx eQTL data via LDlinkR

In myles-lewis/locuszoomr: Gene Locus Plot with Gene Annotations

Obtain GTEx eQTL data via LDlinkR

Description

Adds eQTL (expression quantitative trait loci) information from GTEx (https://gtexportal.org/) to a 'locus' class object. It queries LDlink (https://ldlink.nci.nih.gov/) via the LDlinkR package to retrieve GTEx eQTL information on a reference SNP.

Usage

link_eqtl(loc, pop = "CEU", r2d = "r2", token = "", ...)

Arguments

loc	Object of class 'locus' generated by locus()
pop	A 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU". Passed to LDlinkR::LDexpress().
r2d	Either "r2" for LD r^2 or "d" for LD D', default = "r2". Passed to LDlinkR::LDexpress().
token	Personal access token for accessing 1000 Genomes LD data via LDlink API. See LDlinkR package documentation.
...	Optional arguments such as genome_build which are passed on to LDlinkR::LDexpress()

Details

The additional eQTL information obtained from LDlink web server can be displayed using eqtl_plot() which generates a scatter plot with gene tracks similar to a locus plot, or with overlay_plot() which tries to overlay the EQTL analysis over the original locus results (e.g. GWAS).

Value

Returns an object of class 'locus' with an extra list element 'LDexp' containing a dataframe of information obtained via LDexpress().

See Also

locus() eqtl_plot() overlay_plot()

myles-lewis/locuszoomr documentation built on Nov. 29, 2024, 4:49 p.m.