Message-ID: <5AF9A393.10506@jhu.edu>
Date: 2018-05-14T14:56:19Z
From: Jack Fu
Subject: [Bioc-devel] GenomicRanges List subclass and apply
In-Reply-To: <CAOQ5Nyd5Luay8DUWg9V86A6x=MihKtycBtdd=_w2TXfxbtbLag@mail.gmail.com>
Hi Michael,
Mostly for sending each element of the GRanges object to a custom
function that runs an identical analysis on each element.
I have some functions that take as input a single range -> calculate
number of reads that overlap the range -> subset the range into K number
of segments based on coverage patterns across the range.
Thanks!
Jack
Michael Lawrence wrote:
> Just out of curiosity, why are you looping over a GRanges in the first place?
>
> On Mon, May 14, 2018 at 7:28 AM, Jack Fu<jfu14 at jhu.edu> wrote:
>> Hey all,
>>
>> I think some of the recent changes to GRanges has affected using the
>> apply class functions with GRanges objects:
>>
>> o GenomicRanges now is a List subclass. This means that GRanges objects
>> and their derivatives are now considered list-like objects (even though
>> [[ don't work on them yet, this will be implemented in Bioconductor 3.8).
>>
>>
>> The following code will throw:
>> gr<- GRanges(1, IRanges(1:2, 3:4))
>> sapply(gr, print)
>>
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function 'getListElement' for
>> signature '"GRanges"'
>>
>> Access using gr[1], gr[1:2] still works normally.
>> Are there any recommendations on a workaround for this issue without
>> resorting back to for loops?
>>
>> Thanks all,
>> Jack
>>
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>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
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>>
>
>
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