computeSurvivalPValueForGenePairSet.output {cancerGI}

Survival analysis for pairs of genes

Description

This function counts the number of individuals with different mutation patterns, estimates the median survival time for each mutation pattern, and computes the p values.

Usage

computeSurvivalPValueForGenePairSet.output(file.out, 
	gene.pairs, data.mut, data.surv, 
	colTime = 2, colStatus = 3, 
	type.gene1 = (-1), type.gene2 = (-1), 
	groups = c("All", "Two"), 
	PRINT = FALSE, PRINT.INDEX = FALSE)

Arguments

file.out

Output filename.

gene.pairs

Matrix of two columns, which are gene names.

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 do not need to 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.

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.

Value

Data frame containing the following columns (if groups="Two"):

gene1

gene2

nSingleMut

No. of cases with single mutation

nDoubleMut

No. of cases with double mutation

obsSingleMut

No. of deceased cases with single mutation

obsDoubleMut

No. of deceased cases with double mutation

expSingleMut

Expected no. of deceased cases with single mutation

expDbouleMut

Expected no. of deceased cases with double mutation

medianSingleMut

Estimated median survival time for single mutation

medianDoubleMut

Estimated median survival time for double mutation

pValue

p value for testing whether double/single mutation is associated with survival

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

Examples

## Not run: 
data (mutations)
data (survival)

# compute p values for gene pairs tested in the RNAi knockdown assay
data (tested_pairs)

# compute p values for the gain & loss combination
# and compare only cases of single mutations with cases of double mutations;
# results are written to file tmp.txt under current directory
computeSurvivalPValueForGenePairSet.output (file.out="tmp.txt", 
	tested_pairs, data.mut=mutations, data.surv=survival, 
	type.gene1=1, type.gene2=(-1), groups="Two")


## End(Not run)