geneprofile: Expression plot for selected genes

In maanova: Tools for analyzing Micro Array experiments

Description

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.

Usage

geneprofile(anovaobj, term, geneidx,
            col="blue", type="b", ylim, xlab, ylab, ...)

Arguments

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.

Author(s)

Hao Wu

Examples

# load in data
data(abf1)
# fit the anova model
## Not run: 
fit.fix = fitmaanova(abf1,formula = ~Strain)
# test Strain effect 
test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
# pick significant genes - pick the genes selected by Fs test
idx <- volcano(test.fix)$idx.Fs
geneprofile(fit.fix, "Strain", idx)
## End(Not run)

maanova documentation built on Nov. 8, 2020, 8:21 p.m.