Dear Bioc developers,
I am currently analysing pairwise genome alignments with Bioconductor,
and I represent them with a GRanges object of the first genome,
containing one element by alignment block, and storing the coordinates
in the other genome in a metadata column containing another GRanges object.
Something like this.
GRanges object with 36582 ranges and 2 metadata columns:
seqnames ranges strand | score query
<Rle> <IRanges> <Rle> | <numeric> <GRanges>
[1] S1 162-550 + | 861 XSR:909374-909853
[2] S1 833-3738 + | 7238 XSR:910181-913291
[3] S1 3769-4212 + | 1165 XSR:913510-913953
[4] S1 4246-4381 + | 359 XSR:914134-914275
[5] S1 4532-5990 + | 2977 chr2:6694031-6695569
... ... ... ... . ... ...
[36578] S99 17228-17759 - | 793 chr1:2375870-2376379
[36579] S99 16417-16935 - | 632 chr1:2376612-2377077
[36580] S99 12370-12759 - | 773 chr1:2379949-2380343
[36581] S99 5270-5384 - | 295 chr1:843397-843511
[36582] S99 1949-3053 - | 2105 chr1:845358-846326
-------
Using "Pairwise genome alignment" as a keyword in a search engine, I
found that the packages CNEr is doing something similar, although it
uses a dedicated "GRangePairs" object for the purpose.
Before I start to invest time in either direction, I wanted to check on
that mailing list if there were other solutions already existing, in
particularly closer to the core packages ?
Have a nice day,
Charles
--
Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp
Okinawa Institute of Science and Technology Graduate University
Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu
Toots from work - ~ ~~ ~ - https://mastodon.technology/@charles_plessy
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