qb.remove {qtlbim}R Documentation

Remove or recover qb object and associated MCMC samples

Description

This removes the object and the directory that contains the MCMC samples. It is not enough to remove the R object.

Usage

qb.remove(qbObject, verbose = TRUE)
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).
verbose Print warning 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.ssg.uab.edu/qtlbim

See Also

qb.mcmc, qb.genoprob

Examples

## Not run: 
## 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)

[Package qtlbim version 1.6.0 Index]