[BioC] BAM files to Genomic Ranges object

[Steve Lianoglou]

Hi,

On Tue, Jan 22, 2013 at 10:14 AM,  <jluis.lavin at unavarra.es> wrote:
> Dear all,
>
> I'm afraid I have another question derived from the topic of this post.
> I've used Repitools to calculate Cpg density from my samples, it worked
> correctly, but now when I try to write the density calculations to a file,
> I'm unable...
> Is it possible to do it?
>
> Here's how I tried to do it:
>
> cpdens <- cpgDensityCalc(gr_list, organism=Mmusculus, seq.len = 300)
>
> write.table(cpdens, file = "Cpg_dens.txt", append = FALSE, quote = TRUE,
> sep = "\t", eol = "\n", na = "NA", dec = ".",
> row.names = TRUE, col.names = TRUE)

I've never used Repitools, but:

(1) What is the output of `is(cpdens)` ? If it's not a data.frame,
this won't work
(2) If it is a data.frame, can we see the output of `head(cpdens)` ?

-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