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 |
colTime |
Scalar indicating which column in |
colStatus |
A character string indicating which column in |
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