Question: Problem converting annotation to GenomicRanges object
gravatar for giakountis
21 days ago by
giakountis0 wrote:

Dear community members,

I am new and relatively inexperienced with R and/or this forum so please be patient with my input. I am trying to download gene and exon annotation for human (hg19) and convert it to GenomicRanges object. I am performing the analysis in Windows10,64bit / Rstudio using a Bioconductor package called MetaseqR. It was working fine till I updated to R3.4.3. In brief I have installed the following : 

R version 3.4.3, 64bit, Bioconductor version 3.6 [BiocInstaller 1.28.0], GenomicRanges 1.30.1 [installed from source, Rtools installed in the system-also tried binary 1.30.0 with no effect)

It seems to download the annotation but immediately I get the following error message :

Downloading gene annotation for hg19...
Downloading exon annotation for hg19...
Converting annotation to GenomicRanges object...Error in .find_start_end_cols(df_colnames0, start.field0, end.field0) : cannnot determine start/end columns

Tried downgrading to R3.4.2, R3.4.1 etc to no effect. Tried to run through R gui again the same...Please advice, I am desperate!

ADD COMMENTlink modified 21 days ago • written 21 days ago by giakountis0
Is there a reason that you are trying to build a TxDb package rather than using the already built TxDb.Hsapiens.UCSC.hg19.knownGene package?
ADD REPLYlink written 20 days ago by James W. MacDonald45k

Thanks James for the reply-it is just more automated to do this when you run the metaseqR package. I can (and have done) it manually in the past by downloading the annotation file and feeding it in. I am more curious to know why it stopped working and whether this is a GenomicRanges issue that has to do with its installation. I noticed that the 1.30.1 version that is available as source installation,requires compilation and which is newer compared to the binary (1.30.0), gave several Rd warning messages such as the following :

Rd warning: C:/Users/Local/Temp/Rtmp61SPMD/R.INSTALL1ef81f5f65/XVector/man/XIntegerViews-class.Rd:37: missing file link 'Views'

  Could this be part of the problem?How can i deal with such messages in general?

Many thanks for you time

ADD REPLYlink written 10 days ago by giakountis0

No. The Rd files are the help pages, and wouldn't have anything to do with code functionality.

I doubt this has anything to do with GenomicRanges. The error you see comes from makeGRangesFromDataFrame, which expects there to be a 'start' and 'end' column in the data.frame. If the parser in metaseqr doesn't generate a data.frame with a start and end column, then makeGRangesFromDataFrame will fail.

I tried to look through the code for metaseqr, and it's some legit spaghetti code, so I ran out of patience right quick. The maintainer is supposed to be watching for questions pertaining to their package, but you tagged this question (incorrectly) as a genomicranges question instead of metaseqR. I don't know if you can add that tag at this late date, so you might consider starting another thread with the correct tag.

ADD REPLYlink written 10 days ago by James W. MacDonald45k

Thanks James, I know the maintainer in person, I just wanted to figure out if it is a metaseqR issue or if something else causes the problem.

Many thanks for your time and help!

ADD REPLYlink modified 9 days ago • written 9 days ago by giakountis0

Problem resolved you were right it was a metaseqR bug. Now corrected and runs smoothly, thanks for your time once again!

ADD REPLYlink written 9 days ago by giakountis0
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