Re: [Bioc-devel] Best object structure for representing a pairwise genome alignment ?
Hi Charles, Vince, Herve, A further option would be a DataFrame containing two GRanges columns. This is used for example by the plyranges join_* and pair_* functions. regards, Paul Harrison [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Best object structure for representing a pairwise genome alignment ?
Hi Charles, Vince, Yes, a PairwiseAlignments object will contain the sequences of the 2 genomes being aligned so will be big. Could be mitigated by using one object per chromosome instead of trying to represent the full genome alignment in a single object, but then you loose the ability to represent regions that align across chromosomes. Other downsides of using PairwiseAlignments are: - You loose the nice/simple block-to-block mapping that GRangePairs gives you, together with the easy/straightforward way to annotate the links between blocks (via the metadata columns of the GRangePairs). - A PairwiseAlignments object can only represent replacements and indels while the block-to-block mapping in a GRangePairs object can support rearrangements (in addition to indels and replacements). - The GRangesPairs approach even allows you to represent a many-to-many relationship between the blocks/regions of the 2 genomes, something that a PairwiseAlignments-based approach cannot do. So the GRangePairs approach seems more flexible. Maybe a better way to support an arbitrary relationship between the blocks/regions of the 2 genomes would be to use a 3-slot data structure: 2 slots for 2 GRanges objects defining regions on the 2 genomes + 1 slot for representing the links between the regions defined on each genome (these links could be stored in a Hits object). Note that this is a classic bipartite graph. Would particularly make sense if the mapping between the regions is expected to be many-to-many. This kind of container would be able to represent a side-by-side comparison of 2 arbitrary genomes, in its more general form, not just a pairwise genome alignment, which is more restrictive. Cheers, H. On 9/18/20 02:41, Vincent Carey wrote: > Starting from > > PairwiseAlignments-class package:Biostrings R Documentation > > PairwiseAlignments, PairwiseAlignmentsSingleSubject, and > PairwiseAlignmentsSingleSubjectSummary objects > > Description: > > The ‘PairwiseAlignments’ class is a container for storing a set of > pairwise alignments. > > The ‘PairwiseAlignmentsSingleSubject’ class is a container for > storing a set of pairwise alignments with a single subject. > > The ‘PairwiseAlignmentsSingleSubjectSummary’ class is a container > for storing the summary of a set of pairwise alignments. > > Usage: > > ## Constructors: > ## When subject is missing, pattern must be of length 2 > ## S4 method for signature 'XString,XString' > PairwiseAlignments(pattern, subject, > type = "global", substitutionMatrix = NULL, gapOpening = 0, > gapExtension = 1) > ## S4 method for signature 'XStringSet,missing' > PairwiseAlignments(pattern, subject, > type = "global", substitutionMatrix = NULL, gapOpening = 0, > gapExtension = 1) > ## S4 method for signature 'character,character' > PairwiseAlignments(pattern, subject, > type = "global", substitutionMatrix = NULL, gapOpening = 0, > gapExtension = 1, > baseClass = "BString") > > ... > > my question would be whether this is a relevant starting place? Clearly > the focus is not on coordinates, but perhaps a structure that maintains > genomic content and coordinates together would be of use? > > > On Fri, Sep 18, 2020 at 2:49 AM Charles Plessy > wrote: > >> 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 | scorequery >> | >> [1] S1 162-550 + | 861XSR:909374-909853 >> [2] S1833-3738 + | 7238XSR:910181-913291 >> [3] S1 3769-4212 + | 1165XSR:913510-913953 >> [4] S1 4246-4381 + | 359XSR: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
Re: [Bioc-devel] Best object structure for representing a pairwise genome alignment ?
Starting from
PairwiseAlignments-class package:Biostrings R Documentation
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and
PairwiseAlignmentsSingleSubjectSummary objects
Description:
The ‘PairwiseAlignments’ class is a container for storing a set of
pairwise alignments.
The ‘PairwiseAlignmentsSingleSubject’ class is a container for
storing a set of pairwise alignments with a single subject.
The ‘PairwiseAlignmentsSingleSubjectSummary’ class is a container
for storing the summary of a set of pairwise alignments.
Usage:
## Constructors:
## When subject is missing, pattern must be of length 2
## S4 method for signature 'XString,XString'
PairwiseAlignments(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0,
gapExtension = 1)
## S4 method for signature 'XStringSet,missing'
PairwiseAlignments(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0,
gapExtension = 1)
## S4 method for signature 'character,character'
PairwiseAlignments(pattern, subject,
type = "global", substitutionMatrix = NULL, gapOpening = 0,
gapExtension = 1,
baseClass = "BString")
...
my question would be whether this is a relevant starting place? Clearly
the focus is not on coordinates, but perhaps a structure that maintains
genomic content and coordinates together would be of use?
On Fri, Sep 18, 2020 at 2:49 AM Charles Plessy
wrote:
> 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 | scorequery
> |
>[1] S1 162-550 + | 861XSR:909374-909853
>[2] S1833-3738 + | 7238XSR:910181-913291
>[3] S1 3769-4212 + | 1165XSR:913510-913953
>[4] S1 4246-4381 + | 359XSR: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
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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[Bioc-devel] Best object structure for representing a pairwise genome alignment ?
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 | scorequery | [1] S1 162-550 + | 861XSR:909374-909853 [2] S1833-3738 + | 7238XSR:910181-913291 [3] S1 3769-4212 + | 1165XSR:913510-913953 [4] S1 4246-4381 + | 359XSR: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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
