[Bioc-sig-seq] The "ranges" slot in the sread slot of an AlignedRead class

[Martin Morgan]

Nicolas Delhomme <delhomme at embl.de> writes:

> Hi Martin,
>
> That's what I thought; i was just curious to learn more. Thanks for
> the details!
>
> I should have think of it, as I put it after the session info, that
> most probably my second question will be invisible :-)
>
> I paste it here again:
>
>>
>> And is there an easy way to create a RangesList from an AlignedRead
>> object? I figured out how to do it, but I just want to be sure that I
>> didn't miss it. If it doesn't exist, I think it would be a valuable
>> addition and I could contribute the few lines of code.

Sorry for missing that; I don't think there is anything built-in. We
could exchange your code about introducing something off-list, if you
like.

Martin

> Best wishes,
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> High Throughput Functional Genomics Center
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8426
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
>
>
>
> On 13 May 2009, at 04:30, Martin Morgan wrote:
>
>> Hi Nicolas --
>>
>> Nicolas Delhomme <delhomme at embl.de> writes:
>>
>>> Hi all,
>>>
>>> Well the question is quite easy :-) What does this slot holds?
>>> Because
>>> it looks very different from the actual positions: i.e.
>>>
>>> these are the 10 first ranges
>>>
>>>> sread(aln.clean[chromosome(aln.clean)=="2R"])@ranges[1:10]
>>
>> It's internal to the way reads themselves are stored. sread(aln.clean)
>> returns a DNAStringSet object, the ranges slot of a DNAStringSet
>> points to offsets into a larger DNAString.  As you show later, you
>> want to use position(aln.clean) for alignment information.
>>
>> This representation is meant to be entirely internal to the class. The
>> intention is that the user manipulate objects with defined functions
>> and methods (like position()). Of course the user can get at the
>> contents of slots with @, but there are no guarantees about what will
>> be there if the user does this!.
>>
>> Martin
>>
>>
>>> IRanges object:
>>>      start  end width
>>> [1]   4141 4176    36
>>> [2]   4177 4212    36
>>> [3]   4357 4392    36
>>> [4]   4465 4500    36
>>> [5]   5113 5148    36
>>> [6]   5365 5400    36
>>> [7]   5401 5436    36
>>> [8]   6049 6084    36
>>> [9]   6301 6336    36
>>> [10]  6373 6408    36
>>>
>>> and these are the 10 first positions
>>>
>>>> position(aln.clean[chromosome(aln.clean)=="2R"])[1:10]
>>>  [1]  6419544 18694365 10064416 17228214  5850736 11976428 15335440
>>> 3370962
>>>  [9] 15327509  3366816
>>>
>>>> sessionInfo()
>>> R version 2.9.0 (2009-04-17)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE = en_US .UTF -8
>>> ;LC_NUMERIC = C ;LC_TIME = en_US .UTF -8
>>> ;LC_COLLATE = en_US .UTF -8
>>> ;LC_MONETARY = C ;LC_MESSAGES = en_US .UTF -8
>>> ;LC_PAPER = en_US .UTF -8
>>> ;LC_NAME = C ;LC_ADDRESS
>>> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] ShortRead_1.2.0   lattice_0.17-22   BSgenome_1.12.0
>>> Biostrings_2.12.1
>>> [5] IRanges_1.2.1     rtracklayer_1.4.0 RCurl_0.94-1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] Biobase_2.4.1 grid_2.9.0    hwriter_1.1   tools_2.9.0   XML_2.3-0
>>>
>>> And is there an easy way to create a RangesList from an AlignedRead
>>> object? I figured out how to do it, but I just want to be sure that I
>>> didn't miss it. If it doesn't exist, I think it would be a valuable
>>> addition and I could contribute the few lines of code.
>>>
>>> Best,
>>>
>>> ---------------------------------------------------------------
>>> Nicolas Delhomme
>>>
>>> High Throughput Functional Genomics Center
>>>
>>> European Molecular Biology Laboratory
>>>
>>> Tel: +49 6221 387 8426
>>> Email: nicolas.delhomme at embl.de
>>> Meyerhofstrasse 1 - Postfach 10.2209
>>> 69102 Heidelberg, Germany
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>> -- 
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793