wgaim.asreml {wgaim}R Documentation

wgaim method for class "asreml"

Description

Fits an iterative Whole Genome Average Interval Mapping (wgaim) model for QTL detection

Usage

## S3 method for class 'asreml':
wgaim(baseModel, parentData, TypeI = 0.05, attempts = 5,
                       trace = TRUE, ...)

Arguments

baseModel A model of class "asreml" usually representing a base model with which to build the qtl model.
parentData A data structure that inherits the class "interval" containing the genotypic data as well as the phenotypic data used in the baseModel. This should contain a structure called "full.data" from appropriately merging phenotypic and genotypic data (see read.interval and wmerge).
TypeI The level of significance for detecting a QTL. The default is 0.05.
attempts The number of attempts at convergence for the fixed or random qtl model. The default is 5.
trace An automatic tracing facility. If trace = TRUE then all asreml output is piped to the screen during the analysis. If trace = "file.txt", then output from all asreml models is piped to "file.txt". Both trace machanisms will display a message if a QTL is detected.
... Any other extra arguments to be passed to each of the asreml calls. These may also include asreml.control arguments.

Details

The parentData should contain a data structure "full.data" which consists of a genotypic and phenotypic information appropriately merged (see wmerge.)

As the Whole Genome Average Interval Mapping approach detects QTL's sequentially it may require many calls to asreml. For this reason the function may seem slow and users should be patient.

It is recommended that trace = "file.txt" be used to pipe the sometimes invasive tracing of asreml licensing and fitting numerics for each model to a file. Errors, warnings and messages will still appear on screen during this process. Note some warnings that appear may be passed through from an asreml call and are outputted upon exit. These may be ignored as they are handled during the execution of the function.

To avoid lexcial scoping problems the function also places a version of the "full.data" from parentData into a local data object called "asdata". This ensures that the final model may also be investigated using the methods and features of the asreml package.

Value

An object of class "wgaim" which also inherits the class "asreml" by default. The object returned is actually an asreml object (see asreml.object) with the addition of components from the QTL detection listed below.

QTL A list of components from the significant QTL's detected including a character vector of the significant chromosomes the QTL's were detected in sig.chr and the significant intervals on each chromosome in sig.int. For exploratory purposes the final random effects qtl model is also returned in the component qtlModel.

Author(s)

Julian Taylor, Simon Diffey, Ari Verbyla and Brian Cullis

References

Verbyla, A. P., Cullis, B. R., Thompson, R (2007) The analysis of QTL by simultaneous use of the full linkage map. Theoretical And Applied Genetics, 116, 95-111.

See Also

wmerge, print.wgaim, summary.wgaim

Examples


## Not run: 
# read in data 

data(zinc, package = "wgaim")
data(raccas, package = "wgaim")

# subset linkage map and merge genotypic with phenotypic

raccasS <- subset(raccas, chr = c("1A1", "2D1", "4D2", "6A1"))
raccasM <- wmerge(raccasS, zinc, by = "id")

# base model

zn.fm <- asreml(znconc ~ Type, random = ~ Block + id, data = zinc)

# find QTL's

zn.qtl <- wgaim(zn.fm, parentData = raccasM, trace = "trace.txt",
na.method.X = "include") 
## End(Not run)


[Package wgaim version 0.2 Index]