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PSEUDO -- Program Options
Input Files and Basic Parameters
-f file list - Selects file containing list of data files with family-specific z-score replicates.
-h hypothesis file - Selects hypothesis file with list of affections, lod scores and ranks to test.
-n number of pseudosimuations - Selects the number of pseudosimulations to be run.
-r random seed - Selects a random seed to be used. If none is selected, pseudo will use internal clock time
as a random seed. In either case, the seed used will be listed with other parameter settings in
the output
Additional options
Analysis Options
--balanced -
Sample family replicates evenly when generating pseudosimulations.
--random -
Sample family replicates randomly when generating pseudosimulations.
--chrMax -
Maximum legal chromosome number to input.
Optional Summaries
These options request generation of additional output.
--peaks -
For each unique hypothesis outcome, produce a listing of the maximum lod score on each chromosome for
every simulation. Values will be written to file pseudo.peaks.
--simpeaks -
For each unique hypothesis outcome, produce a listing of the maximum lod score for every simulation.
Values will be written to the file pseudo.simpeaks
--hits -
Output a breakdown of hits by affection variable for each hypothesis. Values will be written to file pseudo.hits.
Family Variance Weights
These options control output of summaries related to family variance weights. The procedure for estimating weights and background pertaining to variance estimation for the replicate pool
method is presented in the section on variance estimation
--reps -
Print a detailed summary of values used to calculate family-specific variance weights, including
proportion of hits by replicate for each family/hypothesis and estimated weights for each family/chromosome.
Values will be written to file pseudo.reps.
--weights -
For each hypothesis, output estimated weights for each family and chromosome. Values will be written to file pseudo.weights.
Output Options
--quiet -
Do not output progress reports while performing long simulations.
--prefix:str -
Change default prefix for output files to str. For instance, pseudo.pdf will be
written to
str.pdf
--pdf -
For each hypothesis, output lod score distributions, distribution of hits and plots of log10(hits per genome) to pseudo.pdf
Memory Usage
--megabytes:n -
Do not attempt to allocate more than n megabytes of memory. Can stop unnecessary crashes on some systems
--diskSpace:n -
Do not attempt to any simulation where diskspace required for any one output file exceeds n megabytes.
Can stop unnecessary crashes on some systems
--thinData:n -
Sample every nth marker when reading in family-specific z-scores.
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