getTopLoadGenes: Extract the relevant genes associated with survival
In survClip: Survival Analysis for Pathways

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

View source: R/getTopGenes.R

Given a survCliques object the function extracts those genes that are the most influent in the PCs identified as significant with a certain threshold.

1	getTopLoadGenes(scObj, thr=0.05, n=5, loadThr=0.6)

`scObj`	an object survCliques
`thr`	threshold to consider a clique as significant. This threshold is used also for the significance of the zscores in zlist
`n`	return up to n top relevant genes
`loadThr`	filter loadings according to 'loadThr' absolute value

Function to reveal those genes that are more relevant in the survival process. The relevance of a gene is based on PC loadings.

a data.frame organized as follows:

featuregene names
clIdclique id
geneLoadgene loading
whichPCthe significant PC where the gene is relevant

All significant cliques are represented. The importance of the genes is expressed by its loading.

Paolo Martini

cliqueSurvivalTest

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]
  cliqueTest <- cliqueSurvivalTest(expr, survAnnot, graph, maxPCs=2)
  getTopLoadGenes(cliqueTest)
}