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jokergoo / rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
https://jokergoo.github.io/rGREAT
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Latest Version Causes Error with Background Set #8

Closed imk1 closed 7 years ago

imk1 commented 7 years ago

I installed the latest version of rGREAT by running devtools::install_github("jokergoo/rGREAT").

I tried to submit a job to GREAT by running job = submitGreatJob(bed, bg=background, species="hg19", bgChoice="data").

I got the following error: Error in .Method(..., deparse.level = deparse.level) : number of columns for arg 2 do not match those of first arg

bed and background each have 3 columns (I checked this using ncol to be sure). Do you know what I might be able to do to fix this problem? Thanks!

jokergoo commented 7 years ago

Can you also sent me the message from traceback()? and also the results from head(bed) and head(background)?

imk1 commented 7 years ago

Here is head(bed): V1 V2 V3 V1 V2 V3 1 chr1 839949 840357 2 chr1 859045 859619 3 chr1 860160 860457 4 chr1 875519 876039 5 chr1 876973 877680 6 chr1 895787 896872

Here is head(background): V1 V2 V3 1 chr1 521497 521667 2 chr1 565226 565412 3 chr1 569315 569501 4 chr1 713854 714383 5 chr1 762393 762557 6 chr1 762605 763202

Here is the output from traceback(): 15: stop("number of columns for arg ", i, " do not match those of first arg") 14: .Method(..., deparse.level = deparse.level) 13: eval(expr, envir, enclos) 12: eval(.dotsCall, env) 11: eval(.dotsCall, env) 10: standardGeneric("rbind") 9: (function (..., deparse.level = 1) standardGeneric("rbind"))(<S4 object of class "DataFrame">, <S4 object of class "DataFrame">) 8: do.call(rbind, lapply(x, mcols, FALSE)) 7: do.call(rbind, lapply(x, mcols, FALSE)) 6: .unlist_list_of_GenomicRanges(args, ignore.mcols = ignore.mcols) 5: .local(x, ..., recursive = recursive) 4: c(gr, setdiff(bg, gr)) 3: c(gr, setdiff(bg, gr)) 2: sort(c(gr, setdiff(bg, gr))) 1: submitGreatJob(bed, bg = background, species = "hg19", bgChoice = "data")

I tried going through the code step-by-step on the command line, and it seems like this line might be causing the problem: https://github.com/jokergoo/rGREAT/blob/master/R/great.R#L179

jokergoo commented 7 years ago

This is a bug caused by the new version of bioconductor packages. I have fixed it. Now you can install the newest version from Github:

devtools::install_github("jokergoo/rGREAT")

Thanks for reporting this!

imk1 commented 7 years ago

Thank you so much for getting this fixed. Everything seems to be working now.