In recognition that there are many factors (genetic loci, macro- genetic factors such as sex, and environmental factors) that influence the extent of environmental variation, the 'vqtl' package conducts genome scans that accommodate and target these factors. The main functions of this package, scanonevar() and scanonevar.perm() take as input a cross object from the popular 'qtl' package.
The 'vqtl' package conducts QTL mapping using an elaboration of the traditional Haley-Knott model. It uses the double generalized linear model (DGLM) to model systematic effects on mean and variance. These systematic effects can be both "nuisance effects" that are uninteresting per se, but are valuable to "correct for" as well as genetic effects which are of immediate interest.
You can install the current stable version of
vqtl from CRAN with:
install.packages(pkgs = 'vqtl')
You can install newer version from github with:
First we'll simulate an
rross object, using a utility from
qtl. Note that we load library
qtl before library
vqtl. This is necessary so that
qtl::scanonevar and not the other way around.
library(qtl)library(vqtl)#> Attaching package: 'vqtl'#> The following object is masked from 'package:qtl':#>#> scanonevarset.seed(27599)test.cross <- qtl::sim.cross(map = qtl::sim.map(len = rep(20, 5), eq.spacing = FALSE))
We'll create two additional columns in the phenotype dataframe and calculate genotype probabilities at each pseudolocus using the Hidden Markov Model provided by
test.cross[['pheno']][['sex']] <- sample(x = c(0, 1),size = qtl::nind(test.cross),replace = TRUE)test.cross[['pheno']][['sire']] <- factor(x = sample(x = 1:5,size = qtl::nind(test.cross),replace = TRUE))test.cross <- qtl::calc.genoprob(cross = test.cross, step = 2)
Now that we have a
cross object that's ready for analysis, we can use the
scanonevar function to conduct a genome scan using the DGLM. Note that we use two formulas -- one for the mean and one for the variancee.
The mean formula must have one variable to the left of the
~ and that variable must be in
cross$pheno. The mean and variance formula can have any number of variables to the right of the
~. Valid variables are (a) in
cross$pheno, (b) the name of a marker, or (c) a special keyword.
The special keywords for mean.formula are
mean.QTL.dom. The special keywords for var.formula are
sov <- scanonevar(cross = test.cross,mean.formula = phenotype ~ sex + D1M2 + mean.QTL.add + mean.QTL.dom,var.formula = ~ sire + D2M3 + var.QTL.add + var.QTL.dom)