for testing rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name' "$title1" '$ppheout' '$ppheout.files_path' '$script_file' Random Normal variate Random Uniform variate Random Gamma variate Random Weibull variate Random exponential variate Random Poisson variate Random categorical choice = #for $n, $f in enumerate($fakePhe) #if $f.series.phetype=='rnorm' {'pN':'$f.pName','pT':'rnorm','pP':"{'Mean':'$f.series.Mean', 'SD':'$f.series.SD'}"} #elif $f.series.phetype=='rgamma' {'pN':'$f.pName','pT':'rgamma','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"} #elif $f.series.phetype=='poisson' {'pN':'$f.pName','pT':'poisson','pP':"{'lamb':'$f.series.lamb',}"} #elif $f.series.phetype=='exponential' {'pN':'$f.pName','pT':'exponential','pP':"{'Mean':'$f.series.Mean',}"} #elif $f.series.phetype=='weibull' {'pN':'$f.pName','pT':'weibull','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"} #elif $f.series.phetype=='cat' {'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'values':'$f.series.values'}"} #elif $f.series.phetype=='unif' {'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'low':'$f.series.low','hi':'$f.series.hi'}"} #end if #end for .. class:: infomark This tool allows you to generate an arbitrary (sort of) synthetic phenotype file with measurements drawn from normal, gamma, weibull, exponential, uniform or categorical distributions. These are for testing under the null hypothesis of no association - the values are random but from user specified distributions. Two output files will appear - one for FBAT and the other for Plink since unfortunately, they have slightly differing requirements for the header row. ----- .. class:: warningmark This tool is very experimental ----- - **Pedigree** is a library pedigree file - the id's will be used in the synthetic null phenotypes - **Title** is a name to give to the output phenotype file On the next page, you can add an unlimited number of various kinds of phenotypes including choices for categorical ones or distributions with specific parameters Just keep using the "Add new phenotype" button to add new specifications until you're done. Use the Execute button to run the program and generate the null phenotype data. The new files will be available on the drop down lists for appropriate tools - eg the FBAT format one will be available if you run the FBAT modelling tool. **Attribution** Originally designed and written for the Rgenetics series of Galaxy tools, and copyright Ross Lazarus 2007 (ross period lazarus at gmail period com) Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html