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


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Timestamp:
Oct 17, 2008, 9:21:23 AM (9 years ago)
Author:
markus
Comment:

--

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  • se.lu.onk.BAFsegmentation

    v22 v23  
    3535
    3636  Windows:
    37   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 ''$R_windows'':
     37  Depending on how you have installed R and Perl on your system you may have to edit the variables ''$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'':
    3838  {{{
     39  ###
    3940  # Mac OS X and Linux
    40   # my $R_command="R --vanilla --no-save --slave < BAF_segment.R";
     41  #my $R_command="R --vanilla --no-save --slave < BAF_segment.R";
     42  ###
    4143  # Windows
     44  # Note that we are using ''Rscript'', which is a part of the R distribution.
    4245  my $R_windows=File::Spec->canonpath('C:/"Program Files"/R/R-2.7.0/bin/Rscript');
    4346  my $R_command="$R_windows --vanilla BAF_segment.R";
    4447  }}}
    45   We have been told that BAFsegmentation has successfully been used in the Cygwin environment with the following ''$R_command'':
    46   {{{
    47   my $R_command="$R_windows --vanilla -f BAF_segment.R";   
    48   }}}
    49 
     48 
    5049''Input data format''
    5150  BAFsegmentation is applied to data for a set of samples in a file that should be tab-delimited in the following format: