Description Usage Arguments Details Value See Also Examples
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.
1 2 3 4 5 6 7 8 9 10 11 | 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)
}
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