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? Thanks! [[alternative HTML version deleted]]

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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793