Question: Problem converting annotation to GenomicRanges object
gravatar for giakountis
9 months 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 9 months ago • written 9 months 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 9 months ago by James W. MacDonald48k

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 9 months 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 9 months ago by James W. MacDonald48k

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 months ago • written 9 months 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 months ago by giakountis0
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