| qb.sweave {qtlbim} | R Documentation |
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.
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)
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. |
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.
Brian S. Yandell, yandell@stat.wisc.edu
## 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)