[BioC] BAM files to Genomic Ranges object

[Steve Lianoglou]

Hi,

On Tue, Jan 22, 2013 at 10:54 AM,  <jluis.lavin at unavarra.es> wrote:
> Hello Steve,
>
> (1) What is the output of `is(cpdens)` ? If it's not a data.frame, this
> won't work
>
> is(cpdens)
> [1] "list"           "vector"         "AssayData"      "vectorORfactor"
>
> head(cpdens)
> .
> .
> .
>
> [99841]  1  3  3  3  4  4  2  2  2  1  0  0  0  0  0  1  1  1  1  1  1  1
> 0  0
> [99865]  2  2  0  0  0  0  0  0  0  3  1  1  0  0  0  0  0  0  0  2  1  1
> 1  0
> [99889]  0  0  0  0  0  0  0  0  0  0  1  1  1  1  1  1  1  1  1  1  1  0
> 0  0
> [99913]  0  3  3  3  3  3  3  3  0  0  0  3  1 13  0  3  2  2  1  0  0  0
> 1  1
> [99937]  0  0  0  2  2  2  2  3  3  1  1  1  1  1  0  0  0  0  0  0  0  2
> 0  2
> [99961]  0  1  0  0  2  2  2  0  0  0  0  0  0  0  0  0  0  0  0  0  1  1
> 1  1
> [99985]  1  0  0  0  0  0  0  1  0  0  0  0  0  0  0
>  [ reached getOption("max.print") -- omitted 3301343 entries ]
>
> It doesn't seem to be data.frame as you pointed out...
> Is it possible write this to an output file of some kind?

Yes, of course.

You just have to ask yourself how you want to serialize it.

?writeLines can be your friend, here, if you want to save it in some
ASCII format.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact