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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