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.
link_eqtl(loc, pop = "CEU", r2d = "r2", token = "", ...)Returns an object of class 'locus' with an extra list element 'LDexp'
containing a dataframe of information obtained via LDexpress().
Object of class 'locus' generated by locus()
A 1000 Genomes Project population, (e.g. YRI or CEU), multiple
allowed, default = "CEU". Passed to LDlinkR::LDexpress().
Either "r2" for LD r^2 or "d" for LD D', default = "r2". Passed
to LDlinkR::LDexpress().
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()
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).
locus() eqtl_plot() overlay_plot()