dlmap-package {dlmap} | R Documentation |
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.
Package: | dlmap |
Type: | Package |
Version: | 1.06 |
Date: | 2010-01-11 |
License: | GPL 2 |
The function dlcross
is a constructor function for dlcross
objects to be input to dlmap.asreml
or dlmap.lme
.
It will read in files in several different formats, including all those
compatible with read.cross
and two new formats to
accommodate association mapping populations and designs with extensive
phenotypic data.
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.
Emma Huang and Andrew George
Maintainer: Emma Huang <Emma.Huang@csiro.au>
Huang, B.E. and George, A.W. 2009. Look before you leap: A new approach to QTL mapping. TAG 119:899-911