[BioC] Need to save an aligned read file using ShortRead package

[Martin Morgan]

On 01/31/2011 12:37 AM, Nazi (Marzieh) Bakhshi wrote:
> Hello,
> 
> I input an aligned read file using readAligned() method in ShortRead
> package:
> 
> file <- "42hr.bowtie"
> aln <- readAligned(file, type = "Bowtie")
> 
> Then I do some modifications on the counts in the aln object, and want to
> output the modified AlignedRead object, either in SAM format, or default
> bowtie output format
> (http://bowtie-bio.sourceforge.net/ma...-bowtie-output<http://bowtie-bio.sourceforge.net/manual.shtml#default-bowtie-output>)
> .
> 
> So now the question is, how can I save the AlignedRead object to the disk in
> either of the aforementioned formats?

For the moment, this must be done 'by hand', e.g., creating a data.frame
with the relevant parts of the AlignedRead class and writing those to
disk with R's standard write.* commands.

Martin

> 
> Thanks!
> 
> 	[[alternative HTML version deleted]]
> 
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