Version 2.0-6 of wgaim is a minor maintenance release to
fix CRAN build warnings.
wgaim is here and it celebrates a
updated release of the package that utilizes the linear mixed modelling
functionality of the R package ASReml-R V4. It should be
noted that this version of wgaim is not compatible with
ASReml-R V3 and users should revert to version 1.4-11 if a
compatible version is required. Within this new version of
wgaim there have been many subtle changes to functions and
their arguments. Most of these changes have been documented below.wgaim.asreml()
has been significantly streamlined for better integration with new
features of ASReml-R V4. Many adjunct wgaim
functions such as mergeData() and
updateWgaim() have been removed. Model updating now occurs
directly using update.asreml().wgaim.asreml(), the phenoData argument has
been removed from the wgaim.asreml call. The data is now
recalled through backwards evaluation of the base model call.wgaim can now handle "f2" cross
objects. This includes the appropriate imputation of missing allele
values through the functionality of cross2int().cross2int() functions arguments have been
changed to more appropriately reflect the nature of the task being
implemented. Specifically, argument missgeno has been
changed to impute and rem.mark has been
changed to consensus.mark.link.map.xxx functions have changed to
linkMap.xxx for better naming consistency with S3
methods.out.stat function has changed to
outStat and has been completely rewritten to use
ggplot2 functionality. See ?outStat for
complete details.vignette("wgaim_intro")outStat(). The
fix now ensures any graphic generated with the function produces the
correct chromosome labels in the appropriate position.gen.type = "interval" is used in
wgaim.asreml().summary.wgaim() when only one
QTL was found.maxiter = 1 from internal
predict.asreml() to prevent spurious output of
non-convergence warnings.cross2int() to remove “.”s from any chromosome names.linkMap.wgaim() was
incorrect and has been amended.out.stat()
have been removed.flanking has been added to the QTL
plotting functions ro ensure that only flanking markers or linked
markers are plotted and highlighted on the linkage map.breakout
argument of wgaim.asreml()."doc" directory of the package. This
can be found on any operating system using the command> system.file("doc", package = "wgaim")
The reference manual contains WGAIM theory and two thorough examples
that show the features of the package. It also contains a “casual walk
through” the package providing the user with a series of 5 steps to a
successful wgaim analysis. - The package now includes three fully
documented phenotypic and genotypic data sets for users to explore. Two
of these three have been used in the manual and scripts that follow the
examples in the manual are available under the “doc” directory of the
package. - The package now provides very efficient whole genome QTL
analysis of high dimensional genetic marker data. All genetic marker
data is passed into wgaim.asreml() through the
"intervalObj" argument. Merging of genotypic and phenotypic
data occurs within wgaim.asreml(). -
wgaim.asreml() has several new arguments related to
selection of QTL. The "gen.type" argument allows the user
to choose a whole genome marker analysis or whole genome mid-point
interval analysis from Verbyla et. al (2007). The "method"
argument gives you the choice of placing QTL in the fixed part of the
linear mixed model as in Verbyla et.al (2007) or the random part of
model as in Verbyla et. al (2012). Finally, the "selection"
argument allows you to choose whether QTL selection is based on whole
genome interval outlier statistics or a two stage process of using
chromosome outlier statistics and then interval outlier statistics. - A
"breakout" argument is now also provided which allows the
user to breakout of the forward selection algorithm at any stage. The
current model along with any calculated QTL components are all available
for inspection. - All linkage map plotting functions can be subsetted by
predefined distances. This includes a list of distances as long as the
number of linkage groups plotted.
wgaim.asreml() to bomb out if
the number of markers was less than the number of genotypes.NaN calculation from sqrt(vatilde) in
qtl.pick().method = "random" was used with the new version of
asreml.cross2int() now accepts R/qtl objects with cross type
"bc","dh","riself".fix.map()
that allowed some co-located sets of markers to appear in the final
reduced linkage map.wgaim.asreml() that quietly destroys the useless
environments that these formula contain.wgaim.asreml() to crash when no
QTL were found.summary.wgaim() to crash when one
QTL was found using method = "random".