help please?

[Pickledzebra]

Hello,

I'm in the position of needing to run quite a few GREAT jobs and thought your package would be life-saver in doing this. However, I am at a complete loss as to why I can't get it to work. I believe I have all the necessary packages installed and I've ensured that I can postForm to the GREAT server.

When I try your simplest example, I get the following:

set.seed(123) bed=circlize::generateRandomBed(nr=1000,nc=0) head(bed) chr start end 1 chr1 155726 2608935 2 chr1 6134977 10483365 3 chr1 11354986 11423447 4 chr1 15134641 19115321 5 chr1 22692774 23328609 6 chr1 23639094 25639077 job=submitGreatJob(bed) Error : Not Found

Error : Not Found

failed with the request, try after 5 min (1th try)

I haven't got the foggiest idea where it is failing.

Thanks!

[jokergoo]

Are you using the newest version of the package? GREAT website recently changed the path of the tool.

library(devtools)
install_github("jokergoo/rGREAT")

[Pickledzebra]

That worked. Thank you so much! However, now I get:

Error in .Primitive("c")(<S4 object of class "Rle">, <S4 object of class "Rle">) : could not find symbol "recursive" in environment of the generic function

This error occurs when I try to include a background (bg) in the function.

job=submitGreatJob(fore,back,species="mm10",bgChoice="data")

fore is an exact subset of back

[jokergoo]

OK, I think the problem is back the background you have. Would you mind send me the objects of fore and back to that I can have a test?

[Pickledzebra]

Yes here they are.

ForeBack.RData.gz

[Pickledzebra]

Any luck with those examples?

[jokergoo]

Strange, I haven't see this error before. With your data, it works fine at my laptop:

> job = submitGreatJob(fore, bg = back, species = "mm10")
Submit time: 2017-12-13 17:26:47
Version: default
Species: mm10
Background: data
Model: Basal plus extension
  Proximal: 5 kb upstream, 1 kb downstream,
  plus Distal: up to 1000 kb
Include curated regulatory domains

Enrichment tables for following ontologies have been downloaded:
  None
> tb = getEnrichmentTables(job)
> length(tb)
[1] 3
> names(tb)
[1] "GO Molecular Function" "GO Biological Process" "GO Cellular Component"
> dim(tb[[1]])
[1] 3489   13

The version of rGERAT I use is 1.11.1

[Pickledzebra]

Ok. So it's some conflict with something else in my R installation, I'm guessing. Thanks so much for the help!