Is range validity checked after GRanges operations?
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Aditya ▴ 160
@aditya-7667
Last seen 21 months ago
Germany

Is range validity checked for when performing range operations on GenomicRanges::GRanges ?

GenomicRanges • 843 views
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Aditya ▴ 160
@aditya-7667
Last seen 21 months ago
Germany

Yes, it is.

Example GenomicRanges:

require(magrittr)
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
granges <- GenomicRanges::GRanges(seqnames = 'chr1', 
                                  ranges   = IRanges::IRanges(start = 100, end = 200), 
                                  strand   = '-', 
                                  seqinfo  = BSgenome::seqinfo(bsgenome))

Coordinates < 1 warn:

GenomicRanges::start(granges) %<>% subtract(500)

Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence chr1. 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.

coordinates > chrlength also do:

GenomicRanges::end(granges) %<>% add(1 + GenomeInfoDb::seqlengths(bsgenome)[['chr1']])

Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 1 out-of-bound range located on sequence chr1. 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.
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Hi Aditya,

Glad you've figured this out.

FWIW note that the toy GRanges object you constructed in your example above can also conveniently be obtained with gr <- GRanges("chr1:100-200:-", seqinfo=seqinfo(bsgenome)).

Cheers,

H.

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Thank you Herve, that's really useful to know!

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