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.
Author(s)
Brian S. Yandell and Elias Chaibub Neto
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