Couldn't connect with MR Base server and error in clumping SNPs using R package

[Tba2024]

Hi,

I am working on a Mendelian randomisation study and when I tried to access the MR Base website I encountered "disconnected from server" for the past two days. I also used the R package but could not clump the SNPs.

Here is the code I used (in a Windows machine).

#I have already set the working directory

options(ieugwasr_api = 'gwas-api.mrcieu.ac.uk/')
library(MRPracticals)
library(TwoSampleMR)
library(ieugwasr)
library(MRInstruments)
library(dplyr)

vignette("MRBase")

data(gwas_catalog)

exposure_gwas <- subset(gwas_catalog, grepl("Low density lipoprotein", Phenotype_simple))
exposure_gwas <- subset(gwas_catalog, grepl("Hoffmann TJ", Author) & Phenotype_simple == "Low density lipoprotein cholesterol levels")

head(exposure_gwas[,c(7:12,18:21)])
exposure_gwas <- subset(exposure_gwas, grepl("EA", Phenotype_info))
head(exposure_gwas[,c(7:12,18:21)])
exposure_gwas<-exposure_gwas[exposure_gwas$pval<5*10^-8,]
exposure_data<-format_data(exposure_gwas)
exposure_data<-clump_data(exposure_data, clump_r2 = 0.001)

#Then I got the following error message
Please look at vignettes for options on running this locally if you need to run many instances of this command.
Clumping suoVAF, 103 variants, using EUR population reference
No encoding supplied: defaulting to UTF-8.
Error in mtfrm.default(list(url = "https://api.opengwas.io/api/ld/clump", :
cannot mtfrm

I saved the options(ieugwasr_api = 'gwas-api.mrcieu.ac.uk/') as .Rprofile in my home directory.
I would be grateful for any suggestion.

[remlapmot]

Please stop using the old API URL - just make sure you have the latest versions of the TwoSampleMR and ieugwasr packages installed.

See https://mrcieu.github.io/ieugwasr/articles/guide.html#authentication for setting up an OPENGWAS_JWT token.