Problem with LDsearch command

[Sandyyy123]

The LD search command was working perfectly until yesterday. I am having the following issue now:

Error in split_to_df(tmp, sep = "\t", fixed = TRUE) :
non-equal lengths for each entry of x post-splitting
In addition: Warning message:
In if (grepl("NCBI", deparse(sys.call()))) { :
the condition has length > 1 and only the first element will be used

[ramiromagno]

@Sandyyy123 could you post a minimal example that illustrates the problem?

[Sandyyy123]

a <- c("rs11776767")
LDSearch(a, dataset = "onekgpilot", panel = "CEU", RSquaredLimit = 0.8,
distanceLimit = 500, GeneCruiser = TRUE, quiet = FALSE)

[Sandyyy123]

Another issue that I had encountered is that if you increase the number of SNPs (>20) in the vector a supplied to the LDSearch command, it fails to give the results

[ramiromagno]

The problem seems to come from upstream, i.e. the SNAP service itself. Particularly if you're asking for the column "Associated Gene Annotations from GeneCruiser" for the output, i.e. option "GA" for the columnList variable. Thus, this call:

http://archive.broadinstitute.org/mpg/snap/ldsearch.php?snpList=rs11776767&hapMapRelease=onekgpilot&hapMapPanel=CEU&RSquaredLimit=0.8&distanceLimit=500000&downloadType=file&includeQuerySnp=on&submit=search&columnList%5B%5D=GA

results in error:

SNP	Proxy	Distance	RSquared	GeneVariant	GeneName	GeneDescription
Error: Server returned HTTP response code: 503 for URL: http://genecruiser.broadinstitute.org/genecruiser3_services/rest/variation/byName?email=gap@broad.mit.edu&name=rs11776767+rs13274017+rs7846449+rs7004998+rs7000939+rs6990055+rs6987200+rs2409649+rs2292371+rs6991526+rs2292370+rs752446+rs6988598+rs2271357+rs7829201+rs7010680+rs1991649+rs6991499+rs7013032+rs2409650+rs7001887+rs6987199+rs11776674+rs13254592+rs6601533+rs7833128+rs1055329+rs10046628+rs6984388+rs6992366+rs6993121+rs7829089+rs11250083+rs11250081+rs2278335+rs1991650+rs6982769&firstResult=0

So the problem should be reported to SNAP (http://archive.broadinstitute.org/mpg/snap/ldsearch.php). You should be able to reproduce this error from the web interface, just make sure "Associated Gene Annotations from GeneCruiser" option is checked down there in the Output Columns.

Nevertheless, this package should probably better handle these errors before they surface down the line...

[ramiromagno]

@Sandyyy123 Regarding that other issue you mentioned about the number of SNPs supplied, it might be better to submit a separate issue, and again, supply a minimal example that shows how exactly it fails.

[sckott]

Another issue that I had encountered is that if you increase the number of SNPs (>20) in the vector a supplied to the LDSearch command, it fails to give the results

@Sandyyy123 this is likely due to a URL that is too long, but do open an issue for that.

tried now, but their server is down - will look at again soon

[Sandyyy123]

Thanks, I am waiting for their server to become functional before I could post the issue. On 27 Feb 2017 22:31, "Scott Chamberlain" <notifications@github.com> wrote: Another issue that I had encountered is that if you increase the number of SNPs (>20) in the vector a supplied to the LDSearch command, it fails to give the results @Sandyyy123 <https://github.com/Sandyyy123> this is likely due to a URL that is too long, but do open an issue for that. tried now, but their server is down - will look at again soon — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#42 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/APr4uVfnIuT6K5PbNZSamkkA1ZGlZPEYks5rg0CzgaJpZM4MMDGE> .

[ramiromagno]

@Sandyyy123 @sckott It seems this issue has been fixed in SNAP.

[Sandyyy123]

Thank you. The issue has now been resolved at the SNAP server.

[sckott]

great, glad to hear