summary.wgaim {wgaim}R Documentation

Summary and print methods for the class "wgaim"

Description

Prints a summary of the "wgaim" object in a presentable format

Usage

## S3 method for class 'wgaim':
summary(object, parentData, ...)

## S3 method for class 'wgaim':
print(x, parentData, ...)

Arguments

object an object of class "wgaim"
x an object of class "wgaim"
parentData A data structure of class "cross" containing the genotypic data as well as the phenotypic data
... further arguments passed to or from other methods

Details

It is important that the parentData is not missing as it contains vital summary information about each of the QTL's detected.

Value

A summary of the QTL component of the "wgaim" object is printed to the screen. For each QTL detected, the summary.wgaim prints which chromosome, name and distance of each flanking marker, size, z-ratio and LOD score. print.wgaim provides a narrative brief of the QTL's detected.

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, 195-211.

See Also

wgaim.asreml

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")

# summarise

print(zn.qtl, raccasM)
summary(zn.qtl, raccasM)

## End(Not run)

[Package wgaim version 0.2 Index]