Hi Morgan It actually works. I should have tried it first. On the other, it's a good thing that you updated the documentation to indicate that this is possible. Many thanks -burak
----- Original Message ---- From: Martin Morgan <[email protected]> To: burak kutlu <[email protected]> Cc: [email protected] Sent: Thursday, August 20, 2009 5:24:04 PM Subject: Re: [Bioc-sig-seq] using shortRead for Bowtie alignments burak kutlu wrote: > Hi Is there a way to specify the actual file name when calling readAligned > for bowtie alignments? Instead of the dirPath? > Thanks Hi Burak -- readAligned("path/to/file", type="Bowtie") but if that is not working for you then perhaps you can provide more information, especially the output of sessionInfo(). As a repeatable example, fl = system.file("extdata", "bowtie", "s_1_aligned_bowtie.txt", package="ShortRead") readAligned(fl, type="Bowtie") I have updated readAligned documentation in the development version. Here's my sessionInfo > sessionInfo() R version 2.9.1 Patched (2009-07-31 r49053) 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] ShortRead_1.2.1 lattice_0.17-25 BSgenome_1.12.3 Biostrings_2.12.8 [5] IRanges_1.2.3 loaded via a namespace (and not attached): [1] Biobase_2.4.1 grid_2.9.1 hwriter_1.1 Martin > -burak > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
