Thanks, Martin.

my sessionInfo is

> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] chipseq_0.1.20     ShortRead_1.3.10   lattice_0.17-22    BSgenome_1.13.6
[5] Biostrings_2.13.11 IRanges_1.3.21

loaded via a namespace (and not attached):
[1] Biobase_2.4.0 grid_2.9.0    hwriter_1.1   tools_2.9.0


On Wed, Jun 3, 2009 at 5:14 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Rebecca --
>
> Rebecca Sun wrote:
> > Hi all,
> >
> > I am in the process of analyzing  ChIP-seq data by using chipseq package.
> > There was an error happen when I use extendRead() to get the longer
> fragment
> > for alignedReads object.
> >
> > ###################
> >> library(ShortRead)
> >> library(chipseq)
> >> aln <-readAligned(".","flowcell.bowtie",type="Bowtie")
> >> unique <-aln[!srduplicated(aln)]
> >> ext <- extendReads(unique, seqLen = 200)
> > *
> > Error in s1[[ipos]] : recursive indexing failed at level 2*
> > ###################
>
> I don't have a fix for this bug, but...
>
> > *
> > I found extendReads() is works when I used it for one AlignedRead:*
> >
> >> ext <-extendReads(unique[1],seqLen=200)
> >> ext
> > $`gi|29823167|ref|NT_010966.13|Hs18_11123`
> > IRanges instance:
> >      start    end width
> > [1] 307249 307448   200
> > [2] 307089 307288   200
> >
> > *And also, I tried to convert aln to GenomeData, then used
> extendread(),no
> > error, but the return value is not IRanges object*
> >> unique_genome <-as(unique,"GenomeData")
> >> ext1<-extendReads(unique_alngenome,seqLen=200)
> >> ext1
> > A GenomeData instance
> > chromosomes(6): gi|29823167|ref|NT_010966.13|Hs18_11123 ...
>
> The members of ext1 are IRanges objects, e.g., ext1[[1]] is an IRanges
> object
>
> > example(readAligned)
> > aln=readAligned(sp, "s_2_export.txt", filter=filt)
> > gd <- extendReads(as(aln, "GenomeData"), 200)
> > gd
> A GenomeData instance
> chromosomes(5): chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa
>
> > gd[[1]]
> IRanges instance:
>         start       end width
> [1]    3393025   3393224   200
> [2]  171119303 171119502   200
>
> [SNIP]
>
> > gd[["chr1.fa"]]
> IRanges instance:
>         start       end width
> [1]    3393025   3393224   200
> [2]  171119303 171119502   200
>
> [SNIP]
>
> My sessionInfo() is
>
> > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-06-02 r48703)
> 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] chipseq_0.1.20     ShortRead_1.3.10   lattice_0.17-25
>  BSgenome_1.13.6
> [5] Biostrings_2.13.12 IRanges_1.3.21
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.5.2 grid_2.10.0   hwriter_1.1
>
>
> what's yours?
>
> Martin
>
>
> > Any suggestion? Thanks.
> >
> > Rebecca
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>

	[[alternative HTML version deleted]]

