ShortRead R package Aligned Read Output??

[nazanin]

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) .

So now the question is, how can I save the AlignedRead object to the disk in either of the aforementioned formats?

Thanks!