geneprofile {maanova} | R Documentation |
This function generate a plot with many lines. Each line represents a gene. The y-axis is the estimated expression level for the given factor from ANOVA model. The x-axis is for the levels of the give factor, e.g., different strains.
geneprofile(anovaobj, term, geneidx, col="blue", type="b", ylim, xlab, ylab, ...)
anovaobj |
An object of class maanova . It should be the
result from fitmaanova . |
term |
The terms to be plotted. |
geneidx |
The index of genes to be plotted. |
col |
The color to be used in plot. |
type |
The line type. |
ylim |
Y-axis limit. |
xlab |
X-axis label. |
ylab |
Y-axis label. |
... |
Other parameters to be passed to
plot . |
Hao Wu hao@jax.org
# load in data data(paigen) # make data object with rep 2 paigen <- createData(paigen.raw, 2) # make an additive model model.add.fix <- makeModel(data=paigen, formula=~Dye+Array+Strain+Diet) # fit ANOVA model anova.add <- fitmaanova(paigen, model.add.fix) # test strain effect ## Not run: test.Strain.fix <- matest(paigen, model.add.fix, term="Strain", n.perm=100) # volcano plot idx <- volcano(test.Strain.fix) # do gene profile for the selected genes geneprofile(anova.add, "Strain", idx$idx.all)## End(Not run)