Plot.sequential: Visualization of sequential decomposition
In hummelma/GlobalAncova: Global test for groups of variables via model comparisons

Description Usage Arguments Note Author(s) See Also Examples

Plot to show the sum of squares decomposition for each gene into parts according to all variables.

1	Plot.sequential(xx, formula, model.dat = NULL, test.genes = NULL, name.geneset = "")

`xx`	Matrix of gene expression data, where columns correspond to samples and rows to genes. The data should be properly normalized beforehand (and log- or otherwise transformed). Missing values are not allowed. Gene and sample names can be included as the row and column names of `xx`.
`formula`	Model formula for the linear model.
`model.dat`	Data frame that contains all the variable information for each sample.
`test.genes`	Vector of gene names or gene indices specifying a gene set.
`name.geneset`	Name of the plotted geneset.

This work was supported by the NGFN project 01 GR 0459, BMBF, Germany.

Ramona Scheufele ramona.scheufele@charite.de
Reinhard Meister meister@tfh-berlin.de
Manuela Hummel m.hummel@dkfz.de
Urlich Mansmann mansmann@ibe.med.uni-muenchen.de

GlobalAncova.decomp, Plot.genes, GlobalAncova

data(vantVeer)
data(phenodata)
data(pathways)

Plot.sequential(vantVeer, formula = ~ ERstatus + metastases + grade, model.dat = phenodata, test.genes = pathways[[3]], name.geneset = "cell cycle pathway")