[Bioc-devel] readGAlignmentPairs with discordant strand
Hervé Pagès
hpages at fredhutch.org
Mon Oct 19 21:00:38 CEST 2015
Hi Michael,
On 10/17/2015 12:01 PM, Michael Lawrence wrote:
> Cool, thanks. So does it make sense to have that as the coercion from
> GAlignmentsList to GAlignmentPairs? I can add it, if it seems
> reasonable. I'm kind of torn on whether a coercion should discard records.
Right, the coercion won't return an object parallel to the input but you
don't have much choice. You could emit a warning to mitigate this.
2 more things:
1) We should refrain from propagating discordant pairs for now. Even
though the GAlignmentPairs container can store them, the API is not
ready. It will be easy to propagate them later. For now, the coercion
method could emit the same kind of warning emitted by
readGAlignmentPairs() about the discordant pairs being dropped.
2) You might want to propagate pairs with
mate_status %in% c("mated", "ambiguous")
instead of "mated" pairs only.
Thanks,
H.
>
> On Sat, Oct 17, 2015 at 8:37 AM, Morgan, Martin
> <Martin.Morgan at roswellpark.org <mailto:Martin.Morgan at roswellpark.org>>
> wrote:
>
> Val and I discussed this a bit, with the resolution that calling the
> GAlignmentPairs() constructor on the first and the second element of
> the GAlignmentsList was the 'easiest' way to go.
>
> ga = unlist(gal[mcols(gal)$mate_status == "mated"])
> GAlignmentPairs(ga[c(TRUE, FALSE)], ga[c(FALSE, TRUE)])
>
> (completely speculative code). If I understand correctly, there's a
> check in for discordant pairs in readGAlignmentPairs, but not in
> GAlignmentPairs itself; could be mistaken though...
>
> Martin
> ________________________________________
> From: Michael Lawrence [lawrence.michael at gene.com
> <mailto:lawrence.michael at gene.com>]
> Sent: Saturday, October 17, 2015 9:48 AM
> To: Hervé Pagès
> Cc: Michael Lawrence; Morgan, Martin; bioc-devel at r-project.org
> <mailto:bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] readGAlignmentPairs with discordant strand
>
> This might have been lost in this thread. If there is an easy way to
> coerce a GAlignmentsList where all(lengths(x) == 2) to a
> GAlignmentPairs, please let me know. Otherwise, I'll add a coerce
> method. Debating whether it should discard elements of length != 2,
> or if it should fail.
>
> On Fri, Oct 16, 2015 at 9:58 AM, Michael Lawrence <michafla at gene.com
> <mailto:michafla at gene.com><mailto:michafla at gene.com
> <mailto:michafla at gene.com>>> wrote:
> Sure, "*" makes more sense for strand, given the precedent.
>
> On Fri, Oct 16, 2015 at 9:55 AM, Hervé Pagès <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org><mailto:hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>>> wrote:
> > On 10/16/2015 09:28 AM, Michael Lawrence wrote:
> >>
> >> I kind of wish it would return NA for things like seqnames and strand,
> >> but yes that would be very useful.
> >
> >
> > Could do this for seqnames() but I'm hesitant to do this for strand().
> > If you look at ?strand in BiocGenerics, ‘*’ is used when the exact
> > strand of the location is unknown, or irrelevant, or when the "feature"
> > at that location belongs to both strands. A pair with discordant strand
> > belongs to both strands. Also there is a lot of code around that
> > assumes strand() never returns NAs.
> >
> >
> > H.
> >
> >>
> >> On Fri, Oct 16, 2015 at 9:15 AM, Hervé Pagès <hpages at fredhutch.org
> <mailto:hpages at fredhutch.org><mailto:hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>>> wrote:
> >>>
> >>> Hi Michael, Martin,
> >>>
> >>> On 10/16/2015 06:48 AM, Michael Lawrence wrote:
> >>>>
> >>>>
> >>>> It does seem like starting with the more general data structure is the
> >>>> better approach, but I couldn't find an easy way to move the paired
> >>>> subset
> >>>> of GAlignmentsList to GAlignmentPairs. You mention a coercion, but it's
> >>>> not
> >>>> obvious to me, unfortunately.
> >>>>
> >>>> Another approach would be a GAlignmentPairs where the unpaired reads
> >>>> have
> >>>> "missing" mates. I know GAlignments has no concept of missing, but it
> >>>> would
> >>>> get everything into a single data structure that is convenient for
> >>>> computing on pairs.
> >>>
> >>>
> >>>
> >>> I could modify readGAlignmentPairs() to have the discordant and/or
> >>> ambiguous pairs end up in th GAlignmentPairs. The ambiguous pairs
> >>> could be marked as such thru a metadata col of the object or thru
> >>> a proper slot. The seqnames() and strand() accessors will return
> >>> * on discordant pairs. Does that sound reasonable?
> >>>
> >>> H.
> >>>
> >>>
> >>>>
> >>>> On Fri, Oct 16, 2015 at 5:21 AM, Morgan, Martin <
> >>>>Martin.Morgan at roswellpark.org
> <mailto:Martin.Morgan at roswellpark.org><mailto:Martin.Morgan at roswellpark.org
> <mailto:Martin.Morgan at roswellpark.org>>> wrote:
> >>>>
> >>>>>
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org
> <mailto:bioc-devel-bounces at r-project.org><mailto:bioc-devel-bounces at r-project.org
> <mailto:bioc-devel-bounces at r-project.org>>] On Behalf
> >>>>>> Of
> >>>>>> Michael Lawrence
> >>>>>> Sent: Friday, October 16, 2015 7:41 AM
> >>>>>> To:bioc-devel at r-project.org
> <mailto:bioc-devel at r-project.org><mailto:bioc-devel at r-project.org
> <mailto:bioc-devel at r-project.org>>
> >>>>>> Subject: [Bioc-devel] readGAlignmentPairs with discordant strand
> >>>>>>
> >>>>>> Now that GAlignmentPairs supports discordant strand between mates, how
> >>>>>> hard would it be to relax that restriction on readGAlignmentPairs()?
> >>>>>>
> >>>>>> Also, would be nice if getDumpedAlignments() returned those dumped by
> >>>>>> readGAlignmentPairs(). Right now, I'm reading a GAlignments (with the
> >>>>>
> >>>>>
> >>>>> extra
> >>>>>>
> >>>>>>
> >>>>>> mcols) and calling makeGAlignmentPairs(). Not so convenient.
> >>>>>
> >>>>>
> >>>>>
> >>>>> I'm not sure whether this is relevant to your use case but
> >>>>> readGAlignmentsList returns a list of paired mates, and if appropriate
> >>>>> (based on ScanBamParam) list elements with solo travelers. The paired
> >>>>> portion of the list can be coerced to GAlignmentPairs if the additional
> >>>>> structure of that class is required.
> >>>>>
> >>>>> Martin
> >>>>>
> >>>>>>
> >>>>>> Michael
> >>>>>>
> >>>>>> [[alternative HTML version deleted]]
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioc-devel at r-project.org
> <mailto:Bioc-devel at r-project.org><mailto:Bioc-devel at r-project.org
> <mailto:Bioc-devel at r-project.org>> mailing list
> >>>>>>https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> This email message may contain legally privileged and/or confidential
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> >>>>> agent responsible for the delivery of this message to the intended
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> >>>>
> >>>> [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-devel at r-project.org
> <mailto:Bioc-devel at r-project.org><mailto:Bioc-devel at r-project.org
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> >>>
> >>> --
> >>> Hervé Pagès
> >>>
> >>> Program in Computational Biology
> >>> Division of Public Health Sciences
> >>> Fred Hutchinson Cancer Research Center
> >>> 1100 Fairview Ave. N, M1-B514
> >>> P.O. Box 19024
> >>> Seattle, WA 98109-1024
> >>>
> >>> E-mail: hpages at fredhutch.org
> <mailto:hpages at fredhutch.org><mailto:hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>>
> >>> Phone: (206) 667-5791
> <tel:%28206%29%20667-5791><tel:%28206%29%20667-5791>
> >>> Fax: (206) 667-1319
> <tel:%28206%29%20667-1319><tel:%28206%29%20667-1319>
> >
> >
> > --
> > Hervé Pagès
> >
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpages at fredhutch.org
> <mailto:hpages at fredhutch.org><mailto:hpages at fredhutch.org
> <mailto:hpages at fredhutch.org>>
> > Phone: (206) 667-5791
> <tel:%28206%29%20667-5791><tel:%28206%29%20667-5791>
> > Fax: (206) 667-1319
> <tel:%28206%29%20667-1319><tel:%28206%29%20667-1319>
>
>
>
> This email message may contain legally privileged and/or
> confidential information. If you are not the intended recipient(s),
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> any disclosure, copying, distribution, or use of this email message
> is prohibited. If you have received this message in error, please
> notify the sender immediately by e-mail and delete this email
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>
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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