[Bioperl-l] data into R from Perl arrays

Yifei Huang huangyifeicmb at gmail.com
Mon Apr 2 20:41:54 EDT 2012


You may try RSPerl.

http://www.omegahat.org/RSPerl/

Yifei

2012/4/2 Florent Angly <florent.angly at gmail.com>

> 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><
> http://search.cpan.org/%**7Efangly/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<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<http://search.cpan.org/%7Efangly/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
>>>>
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>>>>
>>>
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>>
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>
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-- 
Yifei Huang
Department of Biology
McMaster University



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