| wgaim-package {wgaim} | R Documentation |
Whole Genome Average Interval Mapping (wgaim) for QTL detection and estimation
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 <julian.taylor@adelaide.edu.au>
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.