computeSurvivalPValueOneGenePair: Survival analysis for one pair of genes

Description

This function performs survival analysis, similar to function computeSurvivalPValueForGenePairSet.output, but for one pair of genes.

Usage

computeSurvivalPValueOneGenePair(data.mut, data.surv, 
	colTime = 2, colStatus = 3, 
	type.gene1 = (-1), type.gene2 = (-1), 
	groups = c("All", "Two"), 
	compare = c("Both", "Gene1", "Gene2"), 
	PLOT = FALSE, PRINT = FALSE, 
	pvalue.text.x = 10, pvalue.text.y = 0.1, 
	legend.x = 150, legend.y = 1)

Value

The output contains the same info as described in computeSurvivalPValueForGenePairSet.output.

Arguments

data.mut: Integer matrix of individuals by two genes. Each column containing the mutation patterns of multiple genes: 0 as wildtype, 1 amplification and -1 deletion.
data.surv: Data frame containing case ID, survival time and survival status. Cases should match those in data.mut.
colTime: Scalar indicating which column in data.surv contains the survival time.
colStatus: A character string indicating which column in data.surv contains the survival status: "DECEASED" or "LIVING".
type.gene1: Integer indicating the type of mutation: 0 for wild type, 1 for amplification, and -1 for deletion.
type.gene2: Same as type.gene1, but for the second gene.
groups: "All" if comparing all combinations: wildtype & wildtype, wild type & mutated, both mutated; or "Two", if only comparing single mutation and double mutation.
compare: "Both" if comparing all four combinations: wildtype & wildtype, wildtype & mutated, mutated & wildtype, and mutated & mutated. "Gene1" if comparing three combinations: gene1 wildtype, gene1 mutated & gene2 wildtype, and both mutated. "Gene2" is similar to "Gene1".
PLOT: If TRUE, plot the survival curves and print the p value onto the plot. Location of the p value legend is controlled by pvalue.text.x and pvalue.text.y described below.
PRINT: If TRUE, print intermediate values.
pvalue.text.x: The x coordinate of the p value legend in plot.
pvalue.text.y: The y coordinate of the p value legend in plot.
legend.x: The x coordinate of the curve legend in plot.
legend.y: The y coordinate of the curve legend in plot.

Author

Audrey Q. Fu, Xiaoyue Wang

References