sweave: Run sweave to automate QTL search with MCMC samples.

In fboehm/qtlbim: QTL Bayesian Interval Mapping

Description

This routine runs a separate Sweave file (*.Rnw) of commands, making substitutions for the user-supplied data and thresholds. It can be used to automate the search for genetic architecture.

Usage

qb.sweave(cross, pheno.col = 1, n.iter = 3000, n.draws = 64,
  scan.type = "2logBF", hpd.level = 0.5,
  upper.threshold, SweaveFile, SweaveExtra, PDFDir, remove.qb = TRUE)

Arguments

cross	Object of class cross.
pheno.col	Phenotype column in object cross.
n.iter	Number of MCMC iterations to be stored.
n.draws	Number of MC draws to use for fitqtl.
scan.type	Type of 1-D and 2-D scan to perform; see qb.scanone.
hpd.level	Highest probability density level for scan; see qb.hpdone.
upper.threshold	Threshold for upper triangle (epistasis) in 2-D scan; see qb.scantwo.
SweaveFile	Name of Sweave file (default is system.file("doc", "prototype_qtl_hyper_data.Rnw", package = "qtlbim")).
SweaveExtra	Name of user-supplied extra Sweave file (default is NULL).
PDFDir	Name of directory to store PDF files (default is phenoPDF, where pheno is the name associated with phenotype pheno.col).
remove.qb	Remove constucted objects if TRUE.

Details

This is a simple shell around the Sweave routine to create customized documents with embedded QTL analysis. The default file system.file("doc", "prototype.qtl.hyper.slides.Rnw", package = "qtlbim") creates a "beamer" style PDF slide show. An alternative file system.file("external", "prototype.qtl.hyper.paper.Rnw", package = "qtlbim") creates a preprint document. Both require post-processing with pdflatex.

A user-defined section can be added to the automated documents, using the SweaveExtra option. We have provided system.file("external", "hyper.slide.extra.Rnw", package = "qtlbim") for the slide version and system.file("external", "hyper.paper.extra.Rnw", package = "qtlbim") for the preprint version.

Author(s)

Brian S. Yandell, [e-mail]

References

http://www.qtlbim.org

See Also

Sweave

Examples

## Not run: 
data(hyper)

## Create default slide show LaTeX source without extra section.
qb.sweave(hyper)

## Turn LaTeX into PDF. Run twice to get outline correct.
## Need pdflatex on your system.
system("pdflatex prototype.qtl.hyper.slides")
system("pdflatex prototype.qtl.hyper.slides")

## Create document form, with extra section.
qb.sweave(hyper,
  SweaveFile = system.file("external", "prototype.qtl.hyper.paper.Rnw", package = "qtlbim"))
  SweaveExtra = system.file("external", "hyper.paper.extra.Rnw",
    package = "qtlbim"))
system("pdflatex prototype.qtl.hyper.paper")
system("pdflatex prototype.qtl.hyper.paper")

## End(Not run)

fboehm/qtlbim documentation built on Feb. 16, 2021, 12:04 a.m.