ld_search() returns error

[sinarueeger]

Hi, I am trying to extract LD information using the function ld_search() but it keeps returning an error.

> ld_search("rs420358")
Querying SNAP...
Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) : 
  Timeout was reached: Connection timed out after 10005 milliseconds

The url https://www.broadinstitute.org/mpg/snap/index.php seems to have disappeared too.

Maybe these two things are related.

Session Info

```r > devtools::session_info() Session info ---------------------------------------------------------------------------------- setting value version R version 3.5.1 (2018-07-02) system x86_64, darwin15.6.0 ui RStudio (1.1.456) language (EN) collate en_US.UTF-8 tz Europe/Zurich date 2018-08-18 Packages -------------------------------------------------------------------------------------- package * version date source backports 1.1.2 2017-12-13 CRAN (R 3.5.0) base * 3.5.1 2018-07-05 local blogdown 0.8 2018-07-15 CRAN (R 3.5.0) bookdown 0.7 2018-02-18 CRAN (R 3.5.0) compiler 3.5.1 2018-07-05 local crul 0.6.0 2018-07-10 cran (@0.6.0) curl 3.2 2018-03-28 CRAN (R 3.5.0) data.table 1.11.4 2018-05-27 CRAN (R 3.5.0) datasets * 3.5.1 2018-07-05 local devtools 1.13.6 2018-06-27 CRAN (R 3.5.0) digest 0.6.15 2018-01-28 CRAN (R 3.5.0) evaluate 0.11 2018-07-17 CRAN (R 3.5.0) graphics * 3.5.1 2018-07-05 local grDevices * 3.5.1 2018-07-05 local htmltools 0.3.6 2017-04-28 CRAN (R 3.5.0) httpcode 0.2.0 2016-11-14 cran (@0.2.0) knitr 1.20 2018-02-20 CRAN (R 3.5.0) magrittr 1.5 2014-11-22 CRAN (R 3.5.0) memoise 1.1.0 2017-04-21 CRAN (R 3.5.0) methods * 3.5.1 2018-07-05 local plyr 1.8.4 2016-06-08 CRAN (R 3.5.0) R6 2.2.2 2017-06-17 CRAN (R 3.5.0) Rcpp 0.12.18 2018-07-23 CRAN (R 3.5.0) rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0) rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0) rsnps * 0.2.6.9414 2018-08-08 Github (ropensci/rsnps@898bee6) stats * 3.5.1 2018-07-05 local stringi 1.2.4 2018-07-20 CRAN (R 3.5.0) stringr 1.3.1 2018-05-10 CRAN (R 3.5.0) tools 3.5.1 2018-07-05 local triebeard 0.3.0 2016-08-04 cran (@0.3.0) urltools 1.7.1 2018-08-03 cran (@1.7.1) utils * 3.5.1 2018-07-05 local withr 2.1.2 2018-03-15 CRAN (R 3.5.0) xfun 0.3 2018-07-06 CRAN (R 3.5.0) XML 3.98-1.13 2018-08-01 CRAN (R 3.5.0) xml2 1.2.0 2018-01-24 CRAN (R 3.5.0) yaml 2.2.0 2018-07-25 CRAN (R 3.5.0) ```

[sckott]

thx for the report @sinarueeger !

I'll investiage and report back

[sckott]

@sinarueeger sadly Broad Institute has removed the SNAP service. so the ld_search function is now defunct. sorry about that. if you know of a similar place where you can get SNP data you're interested I'm all ears.

[sinarueeger]

Hi @sckott, thanks for letting me know.

I do not know of a service identical to SNAP (I guess the problem is, that these services have to be updated once in a while. Also hosting these large matrices is probably expensive).

But I do know of an alternative called rest.ensembl.org (scroll down to linkage disequilibrium). For example this one. The problem is, that it's often limited to 500KB and when I tried recently, it was not running smoothly (but I'd need to investigate that).

Also, there might be an LDserver in the near future. Someone told me in a reply to an issue here. But I don't know what that would entail.

[sckott]

thanks. I'd be happy to look into adding the ensemble service if you think people would use it. If it's not running well though that could be a reason to avoid it.

[sinarueeger]

I wonder at what date the broadinstitute's SNAP webpage was shut down. If it was already some time ago and I am the first one to notice, then I might have been the only recent user of the ld search function.

[sckott]

hard to say, wish I knew, i imagine there were other users, we have had others ask questions about it, so i think you're not the only