Plot.all {GlobalAncova}R Documentation

Combined visualization of sequential decomposition and influence of single genes on the GlobalAncova statistic

Description

Plot that combines Plot.genes and Plot.sequential into one graphic.

Usage

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

Arguments

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.

Note

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

Author(s)

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

See Also

Plot.genes, Plot.sequential, GlobalAncova.decomp, GlobalAncova

Examples

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

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

[Package GlobalAncova version 3.4.0 Index]