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Bioconductor / VariantAnnotation

Annotation of Genetic Variants
https://bioconductor.org/packages/VariantAnnotation
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Error message from predictCoding () #66

Closed rwanwork closed 2 years ago

rwanwork commented 2 years ago

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 (which I do have FASTA and a GFF for).

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. The error message and warning that I'm getting for predictCoding () is the following:

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 there is something wrong with my data or how I'm using VariantAnnotation, but I don't know where to begin.

The error is stumping me. As for the warning, what is "sequence 2259"? Is that the 2259th sequence in the GFF file? Thank you!

hpages commented 2 years ago

Questions about basic usage of the Bioconductor software are better asked on our support site: https://support.bioconductor.org/ Please make sure to read the posting guide before you post. In particular please provide a minimal reproducible example that illustrates the problem. Other people should be able to simply copy-and-paste the code you show in their own R session in order to reproduce the issue. Finally don't forget to provide your sessionInfo(). Thanks!