Stefan,
In this situation, rather than creating a new class, e.g.
BStringSetList, I would rather encourage use of the pattern() and
subject() extraction function, which return (Quality)AlignedXStringSet
objects, that can then in turn be passed to the aligned method. You will
get the values you are looking for, but without the need for additional
classes. Here is an example:
> library(Biostrings)
> aln <- pairwiseAlignment(c("able", "baker"), c("charlie", "dog"))
> aln[1]
Global PairwiseAlignedXStringSet (1 of 1)
pattern: [1] abl-e
subject: [3] arlie
score: -14.36196
> aln[2]
Global PairwiseAlignedXStringSet (1 of 1)
pattern: [1] bak
subject: [1] dog
score: -36.92151
> aligned(pattern(aln))
A BStringSet instance of length 2
width seq
[1] 5 abl-e
[2] 3 bak
> aligned(subject(aln))
A BStringSet instance of length 2
width seq
[1] 5 arlie
[2] 3 dog
Patrick
On 8/4/10 9:02 AM, Stefan Bentink wrote:
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
<[email protected]> 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
[email protected]
http://www.hsph.harvard.edu/research/stefan-bentink/
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