Changes between Version 40 and Version 41 of se.lu.onk.IlluminaSNPNormalization


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Timestamp:
Oct 17, 2008, 4:29:31 PM (9 years ago)
Author:
markus
Comment:

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  • se.lu.onk.IlluminaSNPNormalization

    v40 v41  
    4747  ###
    4848  # Windows
    49   # Note that we are using ''Rscript'', which is a part of the R distribution.
     49  # Note that we are using Rscript, which is a part of the R distribution.
    5050  my $R_windows=File::Spec->canonpath('C:/"Program Files"/R/R-2.7.0/bin/Rscript');
    5151  my $R_command="$R_windows --vanilla tQN.R";
     
    6060  ||...||...||...||...||...||...||...||...||...||...||
    6161
    62   The data extracted from !BeadStudio needs to be split into a separate file for each sample using the script ''split_beadstudio_samples.pl''.
     62  The data extracted from !BeadStudio needs to be split into a separate file for each sample using the script ''split_samples.pl''.
    6363
    6464  {{{ 
    65     perl split_beadstudio_samples.pl --beadstudio_file=example/example_beadstudio_data.txt
     65    perl split_samples.pl --data_file=example/example_beadstudio_data.txt
    6666  }}}
    6767  where ''example_beadstudio_data.txt'' is a file exported from !BeadStudio in the format described above.
     
    7777  }}}
    7878
    79   This command will perform tQN on the samples in the tQN subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform tQN on a subset of samples you can edit ''sample_names.txt'' accordingly. The normalized data is stored in the tQN subdirectory ''normalized''. For each sample, there is a file with tQN normalized data. A file ''tQN_beadstudio.txt'' is also generated with tQN B allele frequencies and Log R ratios for all samples in a format suitable for import into !BeadStudio using its import sub-column process. tQN also supports generating tQN data for further analysis with PennCNV and QuantiSNP. Running tQN with the following command:
     79  This command will perform tQN on the samples in the tQN subdirectory ''extracted'' that are specified in the file ''sample_names.txt''. If you want to perform tQN on a subset of samples you can edit ''sample_names.txt'' accordingly. The normalized data is stored in the tQN subdirectory ''normalized''. For each sample, there is a file with tQN normalized data. A file ''tQN_beadstudio.txt'' is also generated with tQN B allele frequencies and Log R ratios for all samples in a format suitable for import into !BeadStudio using its import sub-column process. tQN also supports generating tQN data for further analysis with PennCNV, QuantiSNP and BAFsegmentation. Running tQN with the following command:
    8080
    8181  {{{ 
     
    8383  }}}
    8484
    85   generates one data file per sample in the tQN subdirectory ''normalized'' for further analysis using PennCNV. Alternatives for ''--output_format'' are ''QuantiSNP'', which generates one data file per sample for further analysis with QuantiSNP and ''!BeadStudio'', which is the default argument generating the default ''tQN_beadstudio.txt'' file with data for all samples. Beadchip types for which there is a cluster file in the tQN subdirectory ''lib'' are supported by tQN and can be used as alternatives for ''--beadchip''. For PennCNV and QuantiSNP, SNPs having missing values in either B allele frequencies or log R ratios after normalization are excluded from the respective output files.
     85  generates one data file per sample in the tQN subdirectory ''normalized'' for further analysis using PennCNV. Alternatives for ''--output_format'' are ''QuantiSNP'', which generates one data file per sample for further analysis with QuantiSNP, ''BAFsegmentation'', which generates files for further analysis with BAFsegmentation, and ''!BeadStudio'', which is the default argument generating the default ''tQN_beadstudio.txt'' file with data for all samples. Beadchip types for which there is a cluster file in the tQN subdirectory ''lib'' are supported by tQN and can be used as alternatives for ''--beadchip''. For PennCNV and QuantiSNP, SNPs having missing values in either B allele frequencies or log R ratios after normalization are excluded from the respective output files.
    8686   
    8787