qb-internal {qtlbim} | R Documentation |
These are internal qtlbim routines that are made visible in the namespace for technical use.
covar.mean(qbObject, adjust.covar, verbose = FALSE, pheno.col) pull.grid(qbObject, offset, spacing, mask.region, cross, step, off.end, stepwidth, ...) pull.loci(cross, step, off.end, stepwidth, region) qb.cross(qbObject, genoprob = TRUE, ...) qb.cross.class(qbObject) qb.demo() qb.get(qbObject, element, pheno.col, warn = TRUE, ...) qb.load(cross, qbObject, dir, file) qb.save(cross, qbObject, dir, Name) qb.reorder(qbObject, warn = FALSE, pheno.col)
qbObject |
Object of class qb . |
adjust.covar |
Adjustments to covariates. Default is
NA , which adjusts by covariate mean values. Values are
assumed to be in order of fixed covariates. |
verbose |
Verbose mode if TRUE . |
cross |
Object of class cross (see read.cross ). |
offset |
Offset by first marker if TRUE . |
step |
Argument to create.map . |
off.end |
Argument to create.map . |
stepwidth |
Argument to create.map . |
region |
Argument to create.map . |
genoprob |
Compute genotype probabilities with
qb.genoprob if TRUE . |
spacing |
Add columns for map , eq.spacing and
xchr if TRUE . This corresponds to map element
of a scantwo object. |
mask.region |
Subset genome regions if TRUE (see
subset.qb ). |
element |
Character string for element of qbObject to
get. Typically this is a parameter to qb.data ,
qb.model or qb.mcmc , or it is one of the
MCMC sample files in output.dir , from c("iterdiag",
"mainloci", "pairloci", "covariates", "gbye") . |
pheno.col |
Numeric or character identifier for phenotype. Useful eventually for multiple traits. |
warn |
Warn user if qbObject is legacy format if TRUE . |
dir |
Character string name of directory for load if qbObject
does not exist. |
file |
Character string name of file for load if qbObject
does not exist. |
Name |
Character string name of suffix for save if qbObject
exists. |
... |
Additional arguments. |
These are all internal routines. But some may be useful beyond.
qb.demo
is called in demo(qb.tour)
and provides an
interactive selection of the R/qtlbim
demos.
qb.cross
extracts the cross
object associated with
qbObject
. qb.get
is the internal main routine for
extracting information from a qbObject
. As stated elsewhere,
currently qbObject
refers to objects that are critical to it
but not part of it: the cross
object used to create it and the
MCMC samples in files in output.dir
.
covar.mean
finds covariate means or adjusts them to
user-supplied values.
pull.grid
pulls the grid of pseudomarkers from the cross
object associated with qbObject
. The option spacing
determines whether this is in a format similar to
scanone
(FALSE
) or
scantwo
(TRUE
). It is used qb.get
when accessing external MCMC sample files and by several other
routines that require pseudomarker information, notably genotype
probabilities.
qb.reorder
is called by qb.mcmc
to create
pointers to reorder the MCMC samples so that chromosome numbers and
positions within chromosomes are in increasing order. It creates the
subset
element of a qb
object.
qb.save
and qb.load
are depricated. They were used to
save and retrieve MCMC
samples used in examples and vignettes. We now use
save
and data
.
data(qbExample) covar.mean(qbExample) qb.get(qbExample, "output.dir") summary(qb.cross(qbExample)) temp <- qb.get(qbExample, "iterdiag") dim(temp) names(temp) ## Not run: ## The following should have no effect. qbExample <- qb.reorder(qbExampleb) ## You can call the following rather than demo() to get a tour. qb.demo() ## End(Not run)