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FAST / IntegratedReport

Preparing an integrated report file and QQ plots combining the output from several methods in FAST

Note:

   You will need to install perl and the module ‘Statistics::Distributions’ available from 
   http://search.cpan.org/~mikek/Statistics-Distributions-1.02/Distributions.pm

You can install it by following the instructions here

The script FAST.utils.sh provides options to generate a report. Must run ./install.sh first. The options for FAST.utils.sh are:

Option Comments
-p <prefix-to-file <type> QQPlot with 2 arguments, do QQ plots for each method
-r <prefix-to-file> <type> <pvalue-cutoff-for-gene> < pvalue-cutoff-for-SNP> GetReport with 4 arguments, print combined report
type                     : Linear | Logistic | Summary
<pvalue-cutoff-for-gene> : p-value cut off for gene-based tests.  If permutation is not performed, this 
                           will be the percentage of 'significant' genes, ranked by the test statistics.
<p-value cut off for SNP>: p-value cut off for SNP-based tests.  If permutation is not performed, this 
                           will be the percentage of 'significant' genes, ranked by the test statistics.

To combine the results from different methods for analysis and interpretation, you can run the script ./FAST.utils.sh with appropriate options :

Run with the '-r' option as
./FAST.utils.sh -r <prefix-to-file> <type> <pvalue-cutoff-for-gene> < pvalue-cutoff-for-SNP>
e.g ./FAST.utils.sh -r   ./Example/OUT/output   Summary   0.001   0.0001

where <type> can be Linear or Logistic or Summary, and <prefix-to-file> is the path to the prefix of the output files generated by FAST, EXCLUDING the chromosome number 'chrxxx'. It will generate a integrated report file, with suffix report.txt, from the FAST output files for each method combining all the chromosomes that you have run with FAST.

OUTPUT: The output of getReport.pl is a list of genes that reach the significance threshold specified in the command line parameters. A gene will be reported if it has significant p value from at least one of the FAST methods. This list is followed by a list of significant SNPs in the non-transcribed regions. getReport.pl reports all available results from the FAST output files.

EXAMPLE: The following examples takes the FAST output files using the linear model, and reports genes that have gene-based p-value < 0.01 and SNP-based p value < 0.001. Note that only the prefix of the FAST output files EXCLUDING the chromosome number 'chrxxx' is needed.

./FAST.utils.sh -r ./Example/OUT/output Linear 0.01 0.001
./FAST.utils.sh -r ./Example/OUT/output Logistic 0.01 0.001
./FAST.utils.sh -r ./Example/OUT/output Summary 0.01 0.001

These will generate output files : report.Linear.txt , report.Logistic.txt and report.Summary.txt

Note for Beta.FAST: The above methods are not not supported by the new functions in Beta.FAST. Please leave us a note in the Issue Page if you have any suggestions in how to summarize the result of these three methods.

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