wgaim-package {wgaim}R Documentation

Whole Genome Average Interval Mapping (wgaim) for QTL detection

Description

This package uses sophisticated mixed modelling methods with the addition of allowing a whole genome approach to detecting significant QTL's in linkage maps.

Details

Package: wgaim
Type: Package
Version: 1.0
Date: 2008-03-05
License: GPL 2

This package builds on the qtl package of Broman by including additional functions for the modelling and summary of QTL intervals from the full linkage map.

The package provides user friendly functions for the reading in and combining of genotypic and phenorypic data. Specifically, users can read read in genotypic data using read.interval which is a modified version of Bromans read.cross. read.interval performs additional calculations for imputing missing values on each of the chromosomes across the full linkage map and also provides users with genetic distances and recombination fractions for the intervals. Using wmerge the phenotypic data can then be easily merged with the estimated map from read.interval. The returned object from read.interval or wmerge retains the class structure of an object from read.cross for further use with the qtl package if desired.

The package also provides a very neat graphical display of the chromosomes of a "cross" object from read.interval or possibly read.cross. The method function link.map displays the full or subsetted linkage map according to chromosome or distance as well as displays non-overlapping marker names on the left hand side.

Modelling of the QTL's is achieved using the functions wgaim which, as its first argument, requires an asreml base model. As the WGAIM method requires iterative fitting of asreml models users should be patient for results. For convenience the default tracing of results from the asreml models is outputted to a file for further inspection.

Summary and print methods are available for the returned "wgaim" object and provide users with a detailed report on the QTLs, their size, their flanking markers and significance (including LOD score). The returned "wgaim" object may also be plotted using the method function link.map. This function plots the full linkage map subsetted for chromosome and distance as well as provides shaded QTL regions and highlighted flanking markers.

Author(s)

Julian Taylor, Simon Diffey, Ari Verbyla and Brian Cullis Maintainer: Julian Taylor <julian.taylor@csiro.au>

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

qtl-package


[Package wgaim version 0.2 Index]