[Bioc-sig-seq] strand() in ShortRead, Rsamtools

Martin Morgan mtmorgan at fhcrc.org
Sun Feb 28 20:51:34 CET 2010


On 02/28/2010 11:29 AM, Kasper Daniel Hansen wrote:
> Would it not make sense to return a character vector instead of a
> factor?  As we see, factors tends to bit you, and there is no
> particular reason for having a factor in this particular example.

It's ironic in this circumstance, but a factor gives a controlled
vocabulary -- no 'F' / 'R', for instance. Less compelling, representing
a factor takes up less memory than a (vector of) character. Martin

> 
> Kasper
> 
> On Sun, Feb 28, 2010 at 2:03 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> Hi all --
>>
>> I want to be a bit more explicit about a user-visible change that might
>> cause some confusion. This has to do with the development version of
>> ShortRead, and the unreleased version of Rsamtools.
>>
>> Previously, strand() returned levels c("-", "+", "*"). This changed in
>> BSgenome 1.15.10 svn revsion 44085 (2010-01-19). ShortRead didn't catch
>> up to this revision until today (version 1.5.18, revision 44930);
>> Rsamtools caught up in version 0.1.34. Rsamtools also made an important
>> change in the way reads on the reverse strand are handled, see
>> news(package="Rsamtools").
>>
>> Martin
>> --
>> 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
>>
>> _______________________________________________
>> 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



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