Error message from protein coding prediction with VariantAnnotation
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rwan.work • 0
@rwanwork-13888
Last seen 17 days ago
United Kingdom

Hi all,

I'm somewhat new to VariantAnnotation, so perhaps I'm making a simple mistake. But I'm trying to do protein coding prediction with a non-reference genome (i.e., I am providing my own FASTA and GFF files).

So, I'm doing this:

txdb <- makeTxDbFromGFF (file = GFF_FN, dataSource="...", organism="Saccharomyces cerevisiae")
seqinfo <- Seqinfo (seqnames = c(...), seqlengths=c(...), isCircular=c(...), genome="..")
vcf <- readVcf (VCF_FN, seqinfo)
coding <- predictCoding (vcf, txdb, seqSource=SEQ_FN)

where the _FN files are paths to files on my system. Most of the examples I have seen so far have been with human data (i.e., hg19 or hg38). So, I'm not sure if my usage above is correct.

With the last line, I get the following error message and warning:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'seqlevels': unable to find an inherited method for function ‘seqinfo’ for signature ‘"character"’
In addition: Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 2 out-of-bound ranges located on sequence 2259.
  Note that ranges located on a sequence whose length is unknown (NA) or
  on a circular sequence are not considered out-of-bound (use
  seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method` for more information.

I did try to do a search for these messages with Google, but I didn't come up with anything. I guess I'm using one of the earlier functions incorrectly and it is only proteinCoding () that catches it.

As for the warning, what is "sequence 2259"? Is that the 2259th sequence in the GFF file? In my other two inputs (i.e., the genome and the VCF), I don't have 2,259 records -- so my guess is that it is referring to the GFF file, but nothing is jumping out at me on that line.

Any help would be appreciated -- thank you!

Ray

R VariantAnnotation • 79 views
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The code you are showing us is not valid so we can't reproduce the error.

Please see https://github.com/Bioconductor/VariantAnnotation/issues/66#issuecomment-1245779047

Thanks!

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Oh, ok! Sorry for posting in both places -- at first, I posted in GitHub and then I realised it was probably not a bug with the program, but with how I'm using it. So I found this forum.

Thank you for closing that issue for me! I will try to make my example smaller so that the error can be reproduced. Thank you for the advice!

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