Changes between Version 22 and Version 23 of se.lu.onk.BAFsegmentation

Timestamp:

Oct 17, 2008, 9:21:23 AM (16 years ago)

Author:

markus

Comment:

--

se.lu.onk.BAFsegmentation

@@ -35 +35 @@
 
   Windows:
-  Depending on how you have installed R and Perl on your system you may have to edit the variables ''$R_command'' and ''$R_windows'' at the beginning of the file ''BAF_segment_samples.pl''. ''$R_windows'' should likely contain the full path to the R interpreter on your system. Also comment out (with an initial #) the ''$R_command'' used on OS X and Linux systems. For example, we have successfully used BAFsegmentation using !ActivePerl on a Windows system with the following ''$R_windows'':
+  Depending on how you have installed R and Perl on your system you may have to edit the variables ''$R_command'' and ''$R_windows'' at the beginning of the file ''BAF_segment_samples.pl''. ''$R_windows'' should likely contain the full path to the R script interpreter on your system. Also comment out (with an initial #) the ''$R_command'' used on OS X and Linux systems. For example, we have successfully used BAFsegmentation using !ActivePerl on a Windows system with the following ''$R_windows'':
   {{{
+  ###
   # Mac OS X and Linux
-  # my $R_command="R --vanilla --no-save --slave < BAF_segment.R";
+  #my $R_command="R --vanilla --no-save --slave < BAF_segment.R";
+  ###
   # Windows
+  # Note that we are using ''Rscript'', which is a part of the R distribution.
   my $R_windows=File::Spec->canonpath('C:/"Program Files"/R/R-2.7.0/bin/Rscript');
   my $R_command="$R_windows --vanilla BAF_segment.R";
   }}}
-  We have been told that BAFsegmentation has successfully been used in the Cygwin environment with the following ''$R_command'':
-  {{{
-  my $R_command="$R_windows --vanilla -f BAF_segment.R";   
-  }}}
-
+  
 ''Input data format''
   BAFsegmentation is applied to data for a set of samples in a file that should be tab-delimited in the following format: