genius: Function to compute the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010

Description

This function computes the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010. Subtype-specific risk scores are computed for each subtype signature separately and an overall risk score is computed by combining these scores with the posterior probability to belong to each of the breast cancer molecular subtypes.

Usage

genius(data, annot, do.mapping = FALSE, mapping, do.scale = TRUE)

Arguments

data

Matrix of gene expressions with samples in rows and probes in columns, dimnames being properly defined.

annot

Matrix of annotations with at least one column named "EntrezGene.ID", dimnames being properly defined.

do.mapping

TRUE if the mapping through Entrez Gene ids must be performed (in case of ambiguities, the most variant probe is kept for each gene), FALSE otherwise.

mapping

Matrix with columns "EntrezGene.ID" and "probe" used to force the mapping such that the probes are not selected based on their variance.

do.scale

TRUE if the ESR1, ERBB2 and AURKA (module) scores must be rescaled (see rescale), FALSE otherwise.

Value

GENIUSM1Risk score from the ER-/HER2- subtype signature in GENIUS model.
GENIUSM2Risk score from the HER2+ subtype signature in GENIUS model.
GENIUSM3Risk score from the ER+/HER2- subtype signature in GENIUS model.
scoreOverall risk prediction as computed by the GENIUS model.

References

Haibe-Kains B, Desmedt C, Rothe F, Sotiriou C and Bontempi G (2010) "A fuzzy gene expression-based computational approach improves breast cancer prognostication", Genome Biology, 11(2):R18

Examples

Run this code

## load NKI dataset
data(nkis)
## compute GENIUS risk scores based on GENIUS model fitted on VDX dataset
genius.nkis <- genius(data=data.nkis, annot=annot.nkis, do.mapping=TRUE)
str(genius.nkis)
## the performance of GENIUS overall risk score predictions are not optimal
## since only part of the NKI dataset was used