qb-internal: Internal qtlbim routines
In fboehm/qtlbim: QTL Bayesian Interval Mapping

Description Usage Arguments Details Examples

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, drop.duplicates, ...)
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`.
`drop.duplicates`	Drop duplicate chr.pos after roundoff if `TRUE`.
`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)