geneprofile {maanova} | R Documentation

## Expression plot for selected genes

### 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 hao@jax.org

### Examples

    # 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)

[Package maanova version 1.0.0 Index]