main.process: main.process

In survJamda: Survival Prediction by Joint Analysis of Microarray Gene Expression Data

Description

Plot time-dependent ROC curves based on different time points.

Usage

main.process(common.gene, geno.files, surv.data, method = "none", time.dep)

Arguments

common.gene	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

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".

Value

ROC curves plot and AUC values on the plot.

Warning

This function is not called by the user directly.

Author(s)

Haleh Yasrebi

survJamda documentation built on May 1, 2019, 8:50 p.m.