[Bioc-devel] Strand-Awareness for Restrict Function

[Kasper Daniel Hansen]

upstream / downstream is what we have previously used for strand awareness.

Kasper

On Tue, Feb 16, 2016 at 3:41 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Dario,
>
> AFAIK the 'start' and 'end' are strand-independent concepts so it
> wouldn't be a good idea to let the user specify a strand-specific
> window thru these arguments. That means a strand-aware restrict()
> would need to have 2 additional arguments. But how should we name them?
>
> My preference would be to support negative values for 'start' and 'end'
> like we do for subseq(). When negative, the position is counted from
> the end of the sequence (-1 being the last nucleotide). If we had this,
> then you could do your strand-specific trimming with:
>
>   restrict(gr, start=ifelse(strand(gr) == "-", 51, 1),
>                end=ifelse(strand(gr) == "-", -1, -51))
>
> Note that using negative values is convenient but not strictly needed:
>
>   start <- ifelse(strand(gr) == "-", 51, 1)
>   end <- extractROWS(seqlengths(gr), seqnames(gr))
>   end <- ifelse(strand(gr) == "-", end, end - 50)
>   restrict(gr, start=start, end=end)
>
> Cheers,
> H.
>
>
>
> On 02/14/2016 09:00 PM, Dario Strbenac wrote:
>
>> Hello,
>>
>> The restrict function currently has no strand settings. This would be
>> useful if I am creating fixed size windows, 50 bases wide, by sampling the
>> start positions of the windows from a GRanges object. I'd like to restrict
>> the GRanges object being sampled from, but only on the - stand when
>> removing positions 1 to 50 and only on the positive strand when removing
>> positions within the last 50 bases of the chromosome. So, a strand-aware
>> version would be useful, to avoid sampling start positions too close to the
>> ends of chromosomes. I suppose that setdiff will be a suitable alternative,
>> if the first and last 50 bases are calculated of each chromosome.
>>
>> --------------------------------------
>> Dario Strbenac
>> PhD Student
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> 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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>

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