computeSurvivalPValueOneGenePair {cancerGI} | R Documentation |
This function performs survival analysis, similar to function
computeSurvivalPValueForGenePairSet.output
, but for one pair of genes.
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)
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 |
colTime |
Scalar indicating which column in |
colStatus |
A character string indicating which column in |
type.gene1 |
Integer indicating the type of mutation: 0 for wild type, 1 for amplification, and -1 for deletion. |
type.gene2 |
Same as |
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 |
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. |
The output contains the same info as described in computeSurvivalPValueForGenePairSet.output
.
Audrey Q. Fu, Xiaoyue Wang
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
computeSurvivalPValueForGenePairSet.output