qb.remove {qtlbim} | R Documentation |
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.
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, ...)
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 . |
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.
Brian S. Yandell
http://www.qtlbim.org
## 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)