remove: Legacy update, remove or recover of qb object and associated...

In byandell/qtlbim: QTL Bayesian Interval Mapping

Description

Old (2006, R/qtlbim version 2.6) style qb objects had important external objects, namely the cross object and the MCMC samples in flat files that were loaded as needed. qb.legacy upgrades to the new (2007) style qb object. The commands qb.remove and qb.recover are useful to remove and restore old style qb objects.

Usage

qb.legacy(qbObject, remove = FALSE, ...)
qb.remove(qbObject, verbose = TRUE, external.only = FALSE)
qb.recover(cross, traitName, output.dir, n.thin = 40, n.burnin,
  algorithm = "M-H", genoupdate = FALSE, ...)

Arguments

qbObject	Object of class qb (see qb.mcmc).
remove	Remove external MCMC samples if TRUE. This will not remove the cross object associated with the qbObject. Be sure to remove the qbObject itself separately.
verbose	Print warning if TRUE.
external.only	Remove only external MCMC samples if TRUE.
cross	Object of class cross (see read.cross).
traitName	Character string name of trait to recover.
output.dir	Character string with name of output directory (inferred if missing).
n.thin	Thining of MCMC chain used in qb.mcmc.
n.burnin	Burnin of MCMC chain used in qb.mcmc.
algorithm	Algorithm of MCMC chain used in qb.mcmc.
genoupdate	Genotype update flag for MCMC chain used in qb.mcmc.
...	Options passed to qb.data and qb.model.

Details

At the present time, qb.mcmc stores MCMC samples in external files located in directory output.dir, whose name is typically the traitName followed by the date. qb.remove removes this directory along with the qbObject. qb.recover attempts to recover the use of an orphaned output.dir after a crash of R. These are fragile routines.

Author(s)

Brian S. Yandell

References

http://www.qtlbim.org

See Also

qb.mcmc, qb.genoprob

Examples

## Not run: 
## Upgrade legacy qb object.
myqbObject <- qb.legacy(myqbObject)

## Recover qbExample for trait "bp" of cross "hyper" using default output.dir.
qbExample <- qb.recover(hyper, "bp")

## Remove internal qbExample and external output.dir.
qb.remove(qbExample)

## End(Not run)

byandell/qtlbim documentation built on Dec. 19, 2021, 12:47 p.m.