Re^2: Calling R in perl

[blackzero]

Ok, thank you very much to all for the replies. Statistics::R seens to be what I want.

I've installed Statistics::R

But I have some issues.

My code is this:

#!/usr/bin/perl
use strict;
use warnings;
use Statistics::R;

my @lines;
my $line;

my $csv_check = shift @ARGV; #Mark for csv check-----
@ARGV = $csv_check;

while ( defined( $line = <> ) )
{
  push @lines, $line;
}

save_array_output(@lines, ".out");

print "\@lines = \n @lines ";
my $R = Statistics::R->new() ;
  
$R->startR ;
$R -> send('library(genetics);');

$R -> send('table <- read.table("/home/user/my_path/data_freq.txt.out"
+, header=T, row.names=2);');
$R -> send('g1 <- table[, 2];');
$R -> send('meang1 <- mean(g1)');
$R -> send('print(meang1);');

$R -> send('write.table(g1, "/home/user/my_path/g1.txt");');
$R -> send('write.table(meang1, "/home/user/my_path/meang1.txt");');

#my @results1 = get('g1');
print "\@results1 = ", @results1, "\n";

$R->stopR() ;

#-----------------------------------------------
sub save_array_output
{
  @lines = @_;
  my $mid_name = pop @lines; 
  my $output_name = $csv_check.$mid_name;

  open(MYOUTFILE, ">:utf8", $output_name); # Open output file
  print MYOUTFILE "@lines \n";
  close(MYOUTFILE); # Close output file 
}

data_freq.txt is this:

 Locus    Alleles        frequencies
 Bet01 230       0.166666666666666657415 
 Bet01 238       0.500000000000000000000 
 Bet01 244       0.333333333333333314830 
 Bet05 101       0.285714285714285698425 
 Bet05 103       0.500000000000000000000 
 Bet05 105       0.142857142857142849213

I run my program with "./perl-R3.pl data_freq.txt". I am able to call R, activate the genetics package, make it run the file data_freq.txt.out, do the calculations, save the results in "g1.txt" and "meang1.txt".

OK.

But I cant get back g1 to perl.

If I uncomment the line "#my @results1 = get('g1');", I get this error:

Undefined subroutine &main::get called at ./perl-R3.pl line 35.

If I try to pass values from perl to R directly with a command like "$R -> set('table', \@lines);", I also receive an error:

Can't locate object method "set" via package "Statistics::R" at ./perl-R3.pl line ##

Whats the problem here?

Also, if I try to set the work directory to R with a command like "$R -> send('setwd("/home/user/my_path/");');", the program hangs.