cliqueSurvivalTest: Perform survival test on all the cliques of the graph.

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/cliqueSurvivalTest.R

Description

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

Usage

1
2
cliqueSurvivalTest(expr, survAnnot, graph, pcsSurvCoxMethod = c("regular", "sparse"),
alwaysShrink = FALSE, maxPCs = 10, survFormula = "Surv(days, status) ~")

Arguments

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.

Details

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).

Value

A survCliques object.

Author(s)

Paolo Martini

See Also

pathwaySurvivalTest getTopLoadGenes

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
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)
}

survClip documentation built on Nov. 22, 2017, 5:04 p.m.