You can just specify the filename directly as the first argument, so
something like:
readAligned("reads/mut_1_f.fastq.bowtie", type = "Bowtie")
works on the following setup.
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-08-11 r49153)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.3.25 lattice_0.17-25 BSgenome_1.13.10
Biostrings_2.13.32
[5] IRanges_1.3.53
loaded via a namespace (and not attached):
[1] Biobase_2.5.5 grid_2.10.0 hwriter_1.1 tools_2.10.0
On Aug 20, 2009, at 4:45 PM, 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
-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
