pred.time.indep.valid: Prediction of survival time by independent validation.

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

Description

Identify the gene list common to all single data sets and invoke the subsequent function main.process.

Usage

pred.time.indep.valid(geno.files, surv.data, method = "none", time.dep = 0)

Arguments

geno.files	A vector of character strings containing the names of gene expression files.
surv.data	A 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

None.

Author(s)

Haleh Yasrebi

Examples

require(survJamda.data)

data(gse4335)
data(gse3143)
data(gse1992)

data(gse4335pheno)
data(gse3143pheno)
data(gse1992pheno)

geno.files = c("gse4335","gse1992","gse3143")
surv.data = list(c(gse4335pheno[,6],gse1992pheno[,19],gse3143pheno[,4]),
                 c(gse4335pheno[,5],gse1992pheno[,18],gse3143pheno[,3]))
#pred.time.indep.valid(geno.files, surv.data)

## The function is currently defined as
function(geno.files, surv.data)
{
	common.gene = colnames(get(geno.files[1]))
	for (i in 2:length(geno.files))
		common.gene = intersect(common.gene, colnames(get(geno.files[i])))

	par (mfrow = c(1,length(geno.files)))
	par(oma=c(2,2,length(geno.files),2))

	main.process (common.gene, geno.files, surv.data)
  }

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