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
>
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