[Bioc-devel] a warning we may not need any more?

[Hervé Pagès]

Hi Vince,

Good idea. I made that change in GenomeInfoDb 1.1.26:

   library(GenomeInfoDb)
   x <- Seqinfo(seqnames=c("chr1", "chr2", "chr3", "chrM"),
                seqlengths=c(100, 200, NA, 15),
                isCircular=c(NA, FALSE, FALSE, TRUE),
                genome="toy")

   y <- Seqinfo(seqnames=c("chr3", "chr4", "chrM"),
                seqlengths=c(300, NA, 15))

   merge(x, y)  # warning

   genome(y) <- genome(x)[[1]]
   merge(x, y)  # no warning

Cheers,
H.

On 10/09/2014 12:04 PM, Vincent Carey wrote:
> *Warning message:*
>
> *In .Seqinfo.mergexy(x, y) :*
>
> *  Each of the 2 combined objects has sequence levels not in the other:*
>
> *  - in 'x': chr4, chr16, chr10, chr11, chr18, chr20, chr22*
>
> *  - in 'y': chrY*
>
> *  Make sure to always combine/compare objects based on the same reference*
>
> *  genome (use suppressWarnings() to suppress this warning).*
>
>
> *It seems to me that if we can check equality of the assigned genomes, we
> should*
>
> *not issue this warning.*
>
> 	[[alternative HTML version deleted]]
>
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-- 
Hervé Pagès

Program in Computational Biology
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