pathClass (version 0.9.1)

getGeneRanks: Calculate GeneRanks as used by RRFE...

Description

Calculate GeneRanks as used by RRFE

Usage

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

Arguments

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

Value

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

Details

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

References

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

Examples

library(pathClass)
data(example_data)
ranks = getGeneRanks(x, y, mapping=mapping, Gsub=adjacency.matrix)