How to find the BSgenome object that provided the seqinfo of a GRanges object ?
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@charles-plessy-7857
Last seen 8 days ago
Japan

Hello, I construct GRanges objects and pass them the seqinfo of a relevant BSgenome so that I get chromosome sizes. Sometimes, I would like to retrieve the DNA sequence of the ranges programmatically.

Practically it means that, using the information in the GRanges object I need to find the original BSgenome object. For instance, the seqinfo of BSgenome.Scerevisiae.UCSC.sacCer3, leads me to sacCer3 name, and so will do the GRanges objects that are contructed with the same seqinfo.

> BSgenome.Scerevisiae.UCSC.sacCer3 |> genome() |> unique()
[1] "sacCer3"


Is there a Bioc function that, when given "sacCer3" as input would return either the BSgenome object or its name ?

BSgenome • 158 views
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@herve-pages-1542
Last seen 19 hours ago
Seattle, WA, United States

Yup, getBSgenome().