wgaim-package: Whole Genome Average Interval Mapping (wgaim) for QTL...

In wgaim: Whole Genome Average Interval Mapping for QTL Detection and Estimation using ASReml-R

Description

This package provides an efficient computational implementation of the QTL whole genome QTL analysis algorithm (wgaim) discussed in Verbyla et. al (2007, 2012) using extensions of the functionality provided in the linear mixed modelling R package ASReml-R V4.

Details

Package:	wgaim
Type:	Package
Version:	2.0-0
Date:	2019-08-12
License:	GPL 2

Welcome to version 2.0 of wgaim! The documentation given in this help file is only brief and users should consult the vignette available with the package by typing vignette("wgaim") at the prompt. Alternatively, users can also consult the individual help files for the main functions of the package.

The package provides a user friendly function cross2int for the conversion of "cross" objects created using read.cross in Bromans qtl package into an "interval" object ready for use in wgaim. Specifically, cross2int() performs additional calculations to impute missing marker values on each of the chromosomes across the full linkage map and also provides users with genetic distances and recombination fractions for the intervals. The returned object retains the class structure of an object created with read.cross and therefore allows further use with the qtl package if desired.

The package also provides a function for the graphical display of the chromosomes of a "cross" object. The method function linkMap displays the full or subsetted linkage map according to chromosome or distance as well as displays non-overlapping marker names on the right hand side.

QTL analysis is conducted using the function wgaim which, as its first argument, requires an asreml base model. High dimensional genetic components are allowed (See wgaim.asreml for more details). For convenience the default tracing of results from the asreml models can be outputted to a file for further inspection. Outlier statistics and marker effects from each iteration can be viewed using outStat. Diagnostics of the likelihood ratio test performed for each forward step can be displayed using tr.wgaim. The function also displays an incremental probability value matrix of the QTL ascertained at each forward step of the algorithm.

Summary and print methods are available for the returned "wgaim" object and provide users with a detailed report on the QTL, their size, their flanking markers, significance (including LOD score if desired) and approximate contribution to the genetic variance. The returned "wgaim" object may also be plotted using the method function linkMap. This function plots the full linkage map subsetted for chromosome and distance as well as provides shaded QTL regions and highlighted flanking markers. Plotting of QTL for multiple traits is also possible (see linkMap.default).

Author(s)

Julian Taylor and Ari Verbyla Maintainer: Julian Taylor <[e-mail]>

References

Verbyla, A. P & Taylor, J. D, Verbyla, K. L (2012). RWGAIM: An efficient high dimensional random whole genome average (QTL) interval mapping approach. Genetics Research. 94, 291-306.

Julian Taylor, Arunas Vebyla (2011). R Package wgaim: QTL Analysis in Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.

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

wgaim documentation built on Oct. 3, 2019, 9:03 a.m.