NAME

bff-pxf-simulator: A script that creates a JSON array of simulated BFF/PXF

SYNOPSIS

 bff-pxf-simulator [-options]

   Options:
     -f, --format <format>            Format [bff|pxf]
     -n, --number <number>            Set the number of individuals to generate [100]
     -o, --output <file>              Output file [individuals.json]
     --external-ontologies <file>     Path to a YAML file containing ontology terms
     --random-seed <seed>             Initializes pseudorandom number sequences (seed must be an integer)

     --diseases <number>              Set the number of diseases per individual [1]
     --exposures <number>             Set the number of exposures per individual [1]
     --phenotypicFeatures <number>    Set the number of phenotypic features per individual [1]
     --procedures <number>            Set the number of procedures per individual [1]
     --treatments <number>            Set the number of treatments per individual [1]
     --max-[term]-pool <size>         Limit the selection to the first N elements of the term array
     --max-ethnicity-pool <size>      Restrict the ethnicity pool size; each individual will have only one ethnicity

   Generic Options:
     -debug <level>                   Print debugging (from 1 to 5, being 5 max)
     -h, --help                       Brief help message
     -man                             Full documentation
     -v, --verbose                    Verbosity on
     -V, --version                    Print version

DESCRIPTION

This script generates a JSON array of simulated BFF/PXF data. The files can be created based on pre-loaded ontologies or by utilizing an external YAML file.

SUMMARY

A script that creates a JSON array of simulated BFF/PXF.

Implemented array terms:

BFF: diseases, exposures, interventionsOrProcedures, phenotypicFeatures, treatments.

procedures = interventionsOrProcedures

PXF: interventionsOrProcedures, medicalActions.procedure, medicalActions.treatment, phenotypicFeatures.

procedures = medicalActions.procedure

treatments = medicalActions.treatment

INSTALLATION

(only needed if you did not install Pheno-Ranker)

 $ cpanm --sudo --installdeps .

System requirements

  * Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOs, OpenSuse) should do as well.
  * Perl 5 (>= 5.10 core; installed by default in most Linux distributions). Check the version with "perl -v"
  * 1GB of RAM.
  * 1 core (it only uses one core per job).
  * At least 1GB HDD.

HOW TO RUN BFF-PXF-SIMULATOR

When run without any arguments, the software will use default settings. To modify any parameters, please refer to the synopsis for guidance.

If you prefer not to include a specific term in the analysis, set its value to zero. For example:

--treatments 0

Examples:

 $ ./bff-pxf-simulator -f pxf  # BFF with 100 samples

 $ ./bff-pxf-simulator -f pxf -n 1000 -o pxf.json # PXF with 1K samples and saved to pxf.json

 $ ./bff-pxf-simulator -phenotypicFeatures 10 # BFF with 100 samples and 10 pF each

 $ ./bff-pxf-simulator -diseases 0 -exposures 0 -procedures 0 -phenotypicFeatures 0 -treatments 0 # Only sex and ethnicity

COMMON ERRORS AND SOLUTIONS

 * Error message: Foo
   Solution: Bar

 * Error message: Foo
   Solution: Bar

AUTHOR

Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu.

COPYRIGHT AND LICENSE

This PERL file is copyrighted. See the LICENSE file included in this distribution.

cpanm Pheno::Ranker

perl -MCPAN -e shell
install Pheno::Ranker