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