web app error

[Stacey Cherny]

The last few times I've tried to run mrbase from the website, I get this error:

Error! The MR analysis failed:

Error in get(meth)(x$beta.exposure, x$beta.outcome, x$se.exposure, x$se.outcome,  : 

  Please install the mr.raps package using devtools::install_github('qingyuanzhao/mr.raps')

[ph1...@bristol.ac.uk]

Hi Stacey 

Are you still seeing this problem? Did you get a response?

[Charley Budgeon]

I wonder if you have been able to solve this yet? I am getting the same error using the web based app.

Thank you.

[Stacey Cherny]

I set it aside from a while, but trying it now, I get:

Error! The MR analysis failed:

Error in format_radial(b_exp, b_out, se_exp, se_out) : 

  could not find function "format_radial"

R code is:

library(TwoSampleMR)

ao <- available_outcomes()

exposure_dat <- extract_instruments(c('UKB-a:361','UKB-a:362','UKB-a:500'))

exposure_dat <- clump_data(exposure_dat)

outcome_dat <- extract_outcome_data(exposure_dat$SNP, c('299','300','301','302'), proxies = 1, rsq = 0.8, align_alleles = 1, palindromes = 0, maf_threshold = 0.3)

dat <- harmonise_data(exposure_dat, outcome_dat, action = 3)

mr_results <- mr(dat)

[Gibran Hemani]

You may need to install the radial MR package

devtools::install_github("WSpiller/RadialMR")

[Stacey Cherny]

I'm using the mrbase.org website, so I can't install anything.

[g.he...@bristol.ac.uk]

Ah, my mistake. Thanks for letting me know about this, it is updated now and should be working.

[Stacey Cherny]

It is working now, but now I'm getting an error when I try to download the html file and also get an error message for the method comparison plot.

[Stacey Cherny]

I should clarify that the methods plot crashes when I ask for all methods, but if I ask for just the default ones, it does work.

[explode...@gmail.com]

Hey thanks for alerting us to this - recent update failed to install a couple of dependencies. The report should be working now.

wrt the method comparison plot - I think the problem is if you try to display more than 14 methods ggplot throws an error. I will add it to the list of things to fix but for now just recommend choosing the default methods plus any specific ones you might be interested in.