cliqueSurvivalTest: Perform survival test on all the cliques of the graph.
In survClip: Survival Analysis for Pathways

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

if (require(graphite)) {
  data(exp)
  data(survAnnot)
  data(graph)
  row.names(exp) <- paste0("ENTREZID:", row.names(exp))
  genes <- intersect(graph::nodes(graph), row.names(exp))
  graph <- graph::subGraph(genes, graph)
  expr <- exp[genes, , drop=FALSE]
  cliqueSurvivalTest(expr, survAnnot, graph, maxPCs=2)
}