dlmap-package {dlmap}R Documentation

DLMapping for QTL detection

Description

QTL mapping in a mixed model framework with separate detection and localization stages. The former detects the number of QTL on each chromosome based on the genetic variation due to the grouped markers on the chromosome, while the latter stage uses this information to determine the most likely QTL positions. The mixed model can accommodate general fixed and random effects, including spatial effects in field trials and random pedigree effects.

Details

Package: dlmap
Type: Package
Version: 1.0
Date: 2008-11-11
License: GPL 2

Data for the analysis must be input in three files in the following format:

The function dlmap.convert.cross is available to convert other file formats into the appropriate structure and its use is recommended to ensure that the data is properly input.

The primary function is dlmap.asreml, which performs the iterative algorithm to detect and position QTL on all chromosomes with significant genetic variation. This can accomodate sophisticated mixed models for phenotypic variation in addition to the genetic modeling.

Because ASReml-R is proprietary, we provide additional functions for DLMapping using the nlme package to fit mixed models. However, the function dlmap.lme does not provide as many features as that based on ASReml-R.

The vignette included in this package gives more background on the methodology, input file structure, and examples of how to use each of the important functions in the package.

Author(s)

Emma Huang and Andrew George
Maintainer: Emma Huang <Emma.Huang@csiro.au>

References

Huang, B.E. and George, A.W. Look before you leap: A new approach to QTL mapping. Manuscript in preparation

See Also

read.cross, asreml, ibdreg, lme


[Package dlmap version 1.0 Index]