parallel.qtlnet: Code to parallelize use of qtlnet

Description

This routine calls one of four phases in a parallelized version of qtlnet.

Usage

parallel.qtlnet(phase, index = 1, ..., dirpath = ".")

Arguments

phase

Phase of parallelization as number 1 through 4. See details.

index

Index for phase. Used in phases 2 and 4, and for error codes saved in RESULT.phase.index file.

...

Additional arguments for phases. See details.

dirpath

Character string for directory were user can read and write files. When submitting to a cluster, this should remain the default.

Details

See http://www.stat.wisc.edu/~yandell/sysgen/qtlnet for details of implementation in progress. The plan is to run qtlnet via Condor (http://www.condor.org) to scale up to larger networks, say up to 100 nodes. Most important information is passed in files. Phase 1 imports arguments from the params.txt file, which must have parse-able assignments to the arguments of qtlnet:::qtlnet.phase1. This first phase produces file Phase1.RData, which included objects used by all other phases.

Phase 1 also creates file groups.txt, which for each line has begin and end indices for the parents that would result from a call to parents.qtlnet. Phase 2 should be run the same number of times as the number of lines in file groups.txt. Each run produces a bicN.RData file containing BIC computations. These computations are aggregated in Phase 3 to create Phase3.RData, which contains the saved.scores used for mcmc.qtlnet runs in Phase 4, which each produce an mcmcN.RData file. The number of runs of Phase 4 is an argument nruns stored in the params.txt file processed in Phase 1. Finally, Phase 5 aggregates the MCMC results from multiple independent runs into one qtlnet object.

References

Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010) Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes. Ann Appl Statist 4: 320-339. http://www.stat.wisc.edu/~yandell/doc/2010/92.AnnApplStat.pdf

http://www.stat.wisc.edu/~yandell/sysgen/qtlnet

Examples

Run this code

parallel.qtlnet("/u/y/a/yandell/public/html/sysgen/qtlnet/condor", 1)