qb-internal {qtlbim}R Documentation

Internal qtlbim routines

Description

These are internal qtlbim routines that are made visible in the namespace for technical use.

Usage

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)

Arguments

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.

Details

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.

Examples

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)

[Package qtlbim version 1.9.3 Index]