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

[Nicolas Delhomme]

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.

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