parallel.qtlnet {qtlnet} | R Documentation |
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 |
... |
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
(https://research.cs.wisc.edu/htcondor/) 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
http://www.stat.wisc.edu/~yandell/sysgen/qtlnet
See Also
Examples
## Not run:
parallel.qtlnet("/u/y/a/yandell/public/html/sysgen/qtlnet/condor", 1)
## End(Not run)