[Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject

[Stefan Bentink]

Patrick and Kasper,
Thanks for your immediate response. I see the problem. However, 
aligned(pwAligned) would be enough
at least for my application. And it should be possible to implement 
(returning a BStringSetList?) .
Thanks,
Stefan



Patrick Aboyoun wrote:
> Stefan,
> While it would be possible to convert a PairwiseAlignedFixedSubject 
> (all patterns aligned to one subject) object to 
> PairwiseAlignedXStringSet (patterns and subjects are paired during 
> alignments) object, going the direction you are looking for would not 
> be possible. As Kasper mentioned, what can be done instead is adding 
> more methods for PairwiseAlignedXStringSet objects. If you list them 
> out, I'll see what can be done since not all operations, e.g. 
> consensusMatrix, that are applicable to the former class make much 
> sense with the later one.
>
>
> Cheers,
> Patrick
>
>
>
> On 8/4/10 8:12 AM, Kasper Daniel Hansen wrote:
>> Most likely these functions just needs to be implemented for both
>> classes, at least that is what I suspect Patrick will answer.
>>
>> So far you have listed
>>    as.character
>>    bi-directional conversion between the two classes (whihc may or may
>> not make sense)
>>
>> You seem to be alluding to other methods not being implemented.  If
>> that is the case, you should just list all of them, that will make it
>> much easier to fix.
>>
>> Kasper
>>
>> On Wed, Aug 4, 2010 at 11:04 AM, Stefan Bentink
>> <bentink at jimmy.harvard.edu>  wrote:
>>   
>>> Dear List Members,
>>> I'm using the function pairwiseAlignment from the Biostrings package.
>>> Depending on the
>>> input, the function returns either a PairwiseAlignedFixedSubject (if 
>>> you
>>> align a single pattern
>>> with a single subject) or a PairwiseAlignedXStringSet (if you align 
>>> multiple
>>> patterns with one
>>> or more subjects). There are some accessors which work on
>>> PairwiseAlignedFixedSubject
>>> objects but not on PairwiseAlignedXStringSet objects. To use those 
>>> accessors
>>> on a single
>>> element from a PairwiseAlignedXStringSet, one would have to make it a
>>> PairwiseAlignedFixedSubject.
>>> Is there any way to do that? Subsetting doesn't work since it still 
>>> returns
>>> a PairwiseAlignedXStringSet.
>>> Thanks,
>>> Stefan
>>>
>>>
>>> Code example:
>>> library(Biostrings)
>>> pattern1<- c("ACGT")
>>> pattern2<- c("CAGT")
>>> subject1<- c("CAACGTGGAT")
>>> subject2<- c("GAACAGTAAT")
>>>
>>> mat<- nucleotideSubstitutionMatrix(match = 1, mismatch = 0, baseOnly =
>>> FALSE)
>>> pwAligned<-
>>> pairwiseAlignment(c(pattern1,pattern2),c(subject1,subject2),substitutionMatrix=mat,type="local") 
>>>
>>>
>>> ##This throws an error message:
>>> ##as.character(pwAligned[1])
>>> ##how to make pwAligned[1] a PairwiseAlignedFixedSubject?
>>>
>>>
>>>     
>>>> sessionInfo()
>>>>        
>>> R version 2.12.0 Under development (unstable) (2010-04-07 r51635)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] BSgenome.Hsapiens.UCSC.hg19_1.3.16 BSgenome_1.17.6
>>> [3] Biostrings_2.17.26                 GenomicRanges_1.1.19
>>> [5] IRanges_1.7.15
>>>
>>> loaded via a namespace (and not attached):
>>> [1] Biobase_2.9.0 tools_2.12.0
>>>
>>>
>>>
>>>
>>> -- 
>>> Stefan Bentink
>>> Research Fellow
>>> Department of Biostatistics and
>>> Computational Biology
>>> Dana-Farber Cancer Institute
>>> 44 Binney St.
>>> Boston, MA 02115
>>>
>>> Tel: (+1) 617-582-7604
>>> Fax: (+1) 617-582-7760
>>>
>>> bentink at jimmy.harvard.edu
>>> http://www.hsph.harvard.edu/research/stefan-bentink/
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
>>>      
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>>    
>


-- 
Stefan Bentink
Research Fellow
Department of Biostatistics and
Computational Biology
Dana-Farber Cancer Institute
44 Binney St.
Boston, MA 02115

Tel: (+1) 617-582-7604
Fax: (+1) 617-582-7760

bentink at jimmy.harvard.edu
http://www.hsph.harvard.edu/research/stefan-bentink/