dlmap (version 1.13)

dlmap-package: 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:

1.13

Date:

2012-08-09

License:

GPL 2

The function dlcross is a constructor function for dlcross objects to be input to dlmap. It will read in files in several different formats, including the qtl cross format and two new formats to accommodate association mapping populations and designs with extensive phenotypic data.

The primary function is dlmap, 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 the option of using the nlme package to fit mixed models via the algorithm argument. However, there are some features which are only accessible when the algorithm used is asreml.

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.

References

Huang, B.E. and George, A.W. 2009. Look before you leap: A new approach to QTL mapping. TAG 119:899-911

B. Emma Huang, Rohan Shah, Andrew W. George (2012). dlmap: An R Package for Mixed Model QTL and Association Analysis. Journal of Statistical Software 50(6): 1-22. URL http://www.jstatsoft.org/v50/i06/.

See Also

ibdreg, lme