[Bioperl-l] data into R from Perl arrays

Florent Angly florent.angly at gmail.com
Mon Apr 2 18:30:09 EDT 2012


To execute R commands from Perl, you can also try Statistics::R 
(http://search.cpan.org/~fangly/Statistics-R-0.27/lib/Statistics/R.pm 
<http://search.cpan.org/%7Efangly/Statistics-R-0.27/lib/Statistics/R.pm>), 
which has been around for longer, and which I have recently refactored.
Regards,
Florent

On 02/04/12 22:59, Fields, Christopher J wrote:
> Not sure how well it is supported, but there is also Statistics::useR (which has an XS layer for conversing with R).
>
> https://metacpan.org/module/Statistics::useR
>
> chris
>
> On Apr 2, 2012, at 3:17 AM, Adam Witney wrote:
>
>> The quickest way to do this specific example is probably to just save your R commands to a file (eg R_commands.R) and then run some kind of system/exec/backtick function in your perl script to invoke R, something like (untested):
>>
>> #!/usr/bin/perl
>> use strict;
>> use warnings;
>> system( 'R --file R_commands.R' );
>>
>> Alternatively if you want perl and R to be able to interact and pass data back and forth, you could use something like Statistics::R
>>
>> http://search.cpan.org/~fangly/Statistics-R-0.27/lib/Statistics/R.pm
>>
>> HTH
>>
>> adam
>>
>> On 2 Apr 2012, at 06:21, José Ramón Blas Pastor wrote:
>>
>>> Hi,
>>>
>>> a very simple doubt, but I do not know how to manage this.
>>>
>>> I want to plot a histogram for all data in 'datos.txt'.
>>>
>>> a) by using R:
>>> datos<-scan("datos.txt")
>>> pdf("xh.pdf")
>>> hist(datos)
>>> dev.off()
>>>
>>>
>>> b) How could I invoke R inside Perl to do the same??
>>> #!/usr/bin/perl
>>> open(DAT,"datos.txt");
>>> while (<DAT>) {
>>> chomp;
>>> push(@datos,$_);
>>> }
>>> #now I want a histogram of values in @datos
>>>
>>> Thanks!!
>>>
>>> JR
>>>
>>> -- 
>>> José Ramón Blas - PhD
>>> Dept. Biochemistry - Medicine School
>>> University of Castilla-La Mancha
>>> C Almansa, 14
>>> 02006 Albacete (Spain)
>>>
>>> Phone: +34 967599200 ext. 2958
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
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>
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