[BioC] BAM files to Genomic Ranges object

[jluis.lavin at unavarra.es]

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?

Thanks

JL



El Mar, 22 de Enero de 2013, 16:36, Steve Lianoglou escribió:
> 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
>


-- 
Dr. José Luis Lavín Trueba

Dpto. de Producción Agraria
Grupo de Genética y Microbiología
Universidad Pública de Navarra
31006 Pamplona
Navarra
SPAIN