computeSurvivalPValueGenePairAll.output {cancerGI}R Documentation

Survival analysis for pairs of genes (with matched individuals)

Description

This function is similar to computeSurvivalPValueForGenePairSet.output, except that individuals in data.mut and data.surv should match, and that gene.pairs contains four columns: gene1, mutation type of gene1, gene2, mutation type of gene2.

Usage

computeSurvivalPValueGenePairAll.output(file.out, 
	gene.pairs, data.mut, data.surv, 
	colTime = 2, colStatus = 3, 
	groups = c("All", "Two"), 
	PRINT = FALSE, PRINT.INDEX = FALSE)

Arguments

file.out

Output filename.

gene.pairs

Matrix of four columns: gene1, mutation type of gene1, gene2, mutation type of gene2.

data.mut

Integer matrix of genes by cases. The first column contains gene names. Each of the other columns contains mutation patterns of a case: 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".

groups

"All" if comparing all combinations: wildtype & wildtype, wild type & mutated, both mutated; or "Two", if only comparing single mutation and double mutation.

PRINT

Default is FALSE. Prints intermediate values if set to TRUE. Output may be massive if the number of gene pairs is large.

PRINT.INDEX

Default is FALSE. Unused.

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

Called by computeSurvivalPValueForGenePairSet.output


[Package cancerGI version 1.0.0 Index]