survClip (version 0.2.3)

getTopLoadGenes: Extract the relevant genes associated with survival

Description

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

Usage

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

Arguments

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

Value

a data.frame organized as follows:

1. featuregene names

2. clIdclique id

3. geneLoadgene loading

4. whichPCthe significant PC where the gene is relevant

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

Details

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

See Also

cliqueSurvivalTest

Examples

# NOT RUN {
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)
}
# }