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

Description Usage Arguments Details Value See Also Examples

This function performs survival test on given pathway using a matrix with survival annotation

1
2
3

cliqueSurvivalTest(expr, survAnnot, graph,
  pcsSurvCoxMethod = c("regular", "sparse"), alwaysShrink = FALSE,
  maxPCs = 10, survFormula = "Surv(days, status) ~", robust = FALSE)

`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

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)
}