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.*
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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