wgaim-package {wgaim} | R Documentation |
This package uses sophisticated mixed modelling methods with the addition of allowing a whole genome approach to detecting significant QTL's in linkage maps.
Package: | wgaim |
Type: | Package |
Version: | 1.0 |
Date: | 2008-03-05 |
License: | GPL 2 |
This package builds on the qtl package of Broman by including additional functions for the modelling and summary of QTL intervals from the full linkage map.
The package provides user friendly functions for the reading in and
combining of genotypic and phenorypic data. Specifically, users can read
read in genotypic data using read.interval
which is a modified
version of Bromans read.cross
. read.interval
performs additional calculations for imputing missing values on each of the
chromosomes across the full linkage map and also provides users with
genetic distances and recombination fractions for the intervals. Using
wmerge
the phenotypic data can then be easily
merged with the estimated map from read.interval
. The returned
object from read.interval
or wmerge
retains the class structure of an object from read.cross
for further
use with the qtl package if desired.
The package also provides a very neat graphical display of the
chromosomes of a "cross
" object from read.interval
or
possibly read.cross
. The method function link.map
displays
the full or subsetted linkage map according to chromosome or distance as
well as displays non-overlapping marker names on the left hand side.
Modelling of the QTL's is achieved using the functions
wgaim
which, as its first argument, requires an asreml
base model. As the WGAIM method requires iterative fitting of
asreml
models users should be patient for results. For
convenience the default tracing of results from the asreml models is
outputted to a file for further inspection.
Summary and print methods are available for the returned "wgaim
"
object and provide users with a detailed report on the QTLs, their
size, their flanking markers and significance (including LOD score). The
returned "wgaim
" object may also be plotted using the method
function link.map
. This function plots the full linkage map
subsetted for chromosome and distance as well as provides shaded
QTL regions and highlighted flanking markers.
Julian Taylor, Simon Diffey, Ari Verbyla and Brian Cullis Maintainer: Julian Taylor <julian.taylor@csiro.au>
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.