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 <[email protected]> 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 > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
