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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