Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/cliqueSurvivalTest.R
This function performs survival test on given pathway using a matrix with survival annotation.
1 2 | cliqueSurvivalTest(expr, survAnnot, graph, pcsSurvCoxMethod = c("regular", "sparse"),
alwaysShrink = FALSE, maxPCs = 10, survFormula = "Surv(days, status) ~")
|
expr |
expression matrix |
graph |
a graphNEL object |
survAnnot |
a data frame for survival annotations specified according to the survFormuala. The data frame must contain days and status. |
pcsSurvCoxMethod |
a method to perform PCA. A method to perform "regular", "sparse" for regular PCA and sparse PCA, respectively. |
alwaysShrink |
if TRUE, always shrink the covariance matrix. Deafult=FALSE |
maxPCs |
maximum number of PCs used in the Cox formula "Surv(days, status) ~ PC1.." |
survFormula |
the formula to use in coxph analysis. Defaut="Surv(days, status) ~". Please note that the formula end with '~' meaning that PCs will be added. |
Survival test is made according to survFormula. With 'regular' method, a regular PCA analysis is used to compute PCs. With 'sparse' method, a penalized regression is used for the estimation of PCs (as implemented in elasticnet).
A survCliques object.
Paolo Martini
pathwaySurvivalTest
getTopLoadGenes
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