Nothing
pathwaySurvivalTest <- function(expr, survAnnot, graph, pcsSurvCoxMethod=c("regular", "topological", "sparse"),
alwaysShrink=FALSE, maxPCs=10, survFormula = "Surv(days, status) ~"){
genes <- nodes(graph)
genes <- intersect(genes, rownames(expr))
if (length(genes) <= 3){
return(NULL)
warning("Too few genes.")
}
samples <- intersect(colnames(expr),row.names(survAnnot))
if (length(sample) == 0){
return(NULL)
warning("No sample intersection.")
}
survAnnot <- survAnnot[samples,]
expr <- expr[genes,samples, drop=FALSE]
graph <- graph::subGraph(genes, graph)
expr <- expr[genes,, drop=FALSE]
cliques <- clipper:::extractCliquesFromDag(graph)
maxcliques <- max(sapply(cliques, length))
shrink <- length(samples) < maxcliques | alwaysShrink
days <- survAnnot$days
events <- survAnnot$status
method = pcsSurvCoxMethod[1]
res <- pcsSurvCox(genes, expr, survAnnot, method=method, shrink=alwaysShrink, cliques=cliques, maxPCs=maxPCs, survFormula = survFormula)
new("survPath",
pvalue = res$pvalue, zlist = res$zlist, coxObj = res$coxObj, loadings = res$loadings,
method=method)
}
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