Description Usage Arguments Details Value See Also Examples
This function performs survival test on given pathway using a matrix with survival annotation
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expr |
expression matrix |
survAnnot |
a data frame for survival annotations specified according to the survFormula. The data frame must contain days and status |
graph |
a graphNEL object for a graph |
pcsSurvCoxMethod |
a method to perform PCA. Can be "regular", "topological", "sparse" for regular PCA, topological based PCA and sparse PCA, respectively. The latter one (sparse) is particularly suited for cliques only |
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 used in Coxph analysis. Defaut="Surv(days, status) ~". Please note that the formula end with '~' meaning that PCs will be added |
robust |
should be used the robust mode for cox |
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
pathwaySurvivalTest
, getTopLoadGenes
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