getGeneRanks: Calculate GeneRanks as used by RRFE
In pathClass: Classification using biological pathways as prior knowledge

Description Usage Arguments Value Author(s) References Examples

Uses the GeneRank to calculate the ranks for genes. Afterwards the ranks are transformed as needed for the RRFE algorithm.

1 2	getGeneRanks(x, y, mapping, Gsub, method = "foldChange", d = 0.5)

`x`	a p x n matrix of expression measurements with p samples and n genes.
`y`	a factor of length p comprising the class labels.
`mapping`	a mapping that defines how probe sets are summarized to genes.
`Gsub`	an adjacency matrix that represents the underlying biological network.
`method`	see help of summarizeProbes
`d`	the damping factor which controls the influence of the network data and the fold change on the ranking of the genes. Defaults to 0.5

a ranking of the genes for which pathway knowledge was available.

Marc Johannes JohannesMarc@gmail.com

Johannes M, et al. (2010). Integration Of Pathway Knowledge Into A Reweighted Recursive Feature Elimination Approach For Risk Stratification Of Cancer Patients. Bioinformatics

## Not run: 
library(pathClass)
data(example_data)
ranks = getGeneRanks(x, y, mapping=mapping, Gsub=adjacency.matrix)

## End(Not run)

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