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

[Martin Morgan]

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