computeSurvivalPValueOneGenePair.output {cancerGI}

Write results from survival analysis to output for one pair of genes

Description

This function is similar to computeSurvivalPValueOneGenePair, except that it writes the analysis results directly to output file and does not allow for plotting the survival curves.

Usage

computeSurvivalPValueOneGenePair.output(file.out, genes.info, 
	data.mut, data.surv, colTime = 2, colStatus = 3, 
	groups = c("All", "Two"), PRINT = FALSE)

Arguments

file.out

Output filename.

genes.info

A vector of 6 elements: gene1, mutation type, gene2, mutation type, gene1's column index in data.mut, gene2's column index in data.mut.

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.

Value

A vector of values from the survival analysis, 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