Changes between Version 10 and Version 11 of se.lu.onk.BAFsegmentation


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Timestamp:
Sep 17, 2008, 11:19:49 AM (14 years ago)
Author:
markus
Comment:

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  • se.lu.onk.BAFsegmentation

    v10 v11  
    99
    1010=== License ===
    11 The BAFsegmentation software will be available as a stand-alone software package upon acceptance of the paper describing the method, and will become available as
     11The BAFsegmentation software is available as a stand-alone software package, and will become available as
    1212as a plug-in to BASE as the handling of SNP arrays in BASE is developed. Both versions are available under the [http://www.gnu.org/copyleft/gpl.html GNU General Public License].
    1313
     
    1616The method will be downloadable as a stand-alone version soon.
    1717
     18=== How to use BAFsegmentation ===
     19
     20''Requirements''
     21  BAFsegmentation is written in R with a Perl wrapper, so both R and Perl are required. Required Perl modules are: File::Spec, Getopt::Long, IO::File and Pod::Usage (http://www.cpan.org). Required R package is DNAcopy, recommended version is 1.14.0 (http://www.bioconductor.org).
     22
     23''Installation''
     24  Download and unzip the file available under the section ''Download BAFsegmentation'' on this page.
     25
     26  OS X or Linux:
     27  The programs should run as they are. You need R and perl in your path.
     28
     29  Windows:
     30  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'':
     31  {{{
     32  # Mac OS X and Linux
     33  # my $R_command="R --vanilla --no-save --slave < BAF_segment.R";
     34  # Windows
     35  my $R_windows=File::Spec->canonpath('C:/"Program Files"/R/R-2.7.0/bin/Rscript');
     36  my $R_command="$R_windows --vanilla BAF_segment.R";
     37  }}}
     38 
     39
     40''Input data format''
     41  BAFsegmentation is applied to data exported from !BeadStudio. For a set of samples, the file exported from !BeadStudio should be tab-delimited in the following format:
     42  ||Name||Chr||Position||sample1.B Allele Freq||sample1.Log R Ratio||sample2.B Allele Freq||sample2.Log R Ratio||sample3.B Allele Freq||sample3.Log R Ratio||...||
     43  ||rs12354060||1||10004||1||0.110391||1||-0.05188531||1||0.07706165||...||
     44  ||rs2691310||1||46844||0.5519782||0.2984372||0.4636427||0.3640218||0.4393658||0.2589271...||
     45  ||...||...||...||...||...||...||...||...||...||...||
     46
     47  The data extracted from !BeadStudio needs to be split into a separate file for each sample using the script ''split_beadstudio_samples.pl''.
     48
     49  {{{ 
     50    perl split_beadstudio_samples.pl --beadstudio_file=example/example_beadstudio_data.txt
     51  }}}
     52  where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.
     53
     54  This script will generate one file per sample together with a file ''sample_names.txt'' in the BAFsegmentation subdirectory ''extracted''. These files are used when BAFsegmentation is run and can be deleted once the samples are normalized.
     55
     56''Performing BAFsegmentation''
     57
     58  In the BAFsegmentation directory, run BAFsegmentation with the following command:
     59
     60  {{{ 
     61     perl BAF_segment_samples.pl
     62  }}}
     63
     64  This command will perform BAFsegmentation on the samples in the BAFsegmentation subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform BAFsegmentation on a subset of samples you can edit ''sample_names.txt'' accordingly. The segmented data is stored in the BAFsegmentation subdirectory ''segmented''.
     65
    1866=== Supplemental Data ===
    1967
    2068 * The plots referred to in additional data file 4 in the manuscript are available [http://cbbp.thep.lu.se/~markus/publications/papers/BAFsegmentation_supplemental_data.zip here].
    2169 * The simulated data set will be available soon.
     70 * Infinium data for four matched tumor-normal pairs and a dilution series of a tumor cell line mixed with its paired normal cell line are available in NCBI's Gene Expression Omnibus with accession [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11976 GSE11976].
    2271
    2372=== Contact ===