computeSurvivalPValueOneGenePair {cancerGI}

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)

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.

Value

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

Author(s)

Audrey Q. Fu, Xiaoyue Wang

References

Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. doi: 10.1038/ncomms5828

See Also

computeSurvivalPValueForGenePairSet.output