survJamda (version 1.1.4)

featureselection: Apply a feature selection

Description

Apply univariate Cox regression and rank the genes based on the Cox p-value.

Usage

featureselection(gnExpMat, survivaltime, censor, method = "none",gn.nb)

Arguments

gnExpMat

Matrix of gene expression data.

survivaltime

Vector of survival time.

censor

Vector of censoring status. In the censoring status vector, 1 = event occurred, 0 = censored.

method

A character string specifying the feature selection method: "none" for top-ranking or one of the adjusting methods specified by the p.adjust function.

gn.nb

Number of genes to select for gene signature when method="none".

Value

A list of two vectors, the Cox coefficients and Cox p-values.

Warning

This function is not called by the user directly.

Details

In top-ranking, genes are selected based on univariate Cox P-value ranking using the coxph function in the R survival package. In this feature selection method, the genes are ranked based on their likelihood ratio P-value and the top-gn.nb ranked genes with the smallest P-values are retained as the gene signature.

The p.adjust function in the R stats package is used and all adjusted p-values not greater than 0.05 are retained if method != "none".

References

Yasrebi H, Sperisen P, Praz V, Bucher P, 2009 Can Survival Prediction Be Improved By Merging Gene Expression Data Sets?. PLoS ONE 4(10): e7431. doi:10.1371/journal.pone.0007431.