| | 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 | |
