Vector of character strings containing the names of the genes common to all
data sets.
geno.files
Vector of character strings containing the names of expression files.
surv.data
The list of two vectors, survival time and censoring status. In the censoring status vector, 1 = event occurred, 0 = censored.
method
A character string specifying the feature selection method: "none" for top-100 ranking or one of the adjusting methods specified by the p.adjust function
time.dep
An integer 0 or 1, 1 to plot time-dependent ROC curves for different time points and 0 for no plot
Value
ROC curves plot and AUC values on the plot.
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-100 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".