getGenes {pathVar} | R Documentation |
Gets significant genes within a certain window of variability.
getGenes(pvalue_results,pathway,window)
pvalue_results |
output of |
pathway |
A pathway name. |
window |
A |
It takes the result of pathVarTwoSamplesCont
, a given pathway and "window".
It will give you the genes having their variability value in the window for group 1 and another set of genes for group 2 corresponding to the given pathway.
It also returns the set of all the genes from your dataset that belong to this pathway.
An object of class geneSet
with 3 properties. The first 2 are the genes in the window from each group. The third are all the genes.
Laurence de Torrente, Samuel Zimmerman, Jessica Mar
# we run the 2 samples analysis on the first 10 pathways from kegg pways.kegg.10pways <- lapply(pways.kegg, function(x) x[1:10]) results_2samples=pathVarTwoSamplesCont(bock,pways.kegg.10pways,groups=as.factor(c(rep(1,10),rep(2,10)))) genes_window=getGenes(results_2samples,pways.kegg$PATHNAME[10],c(0.25,075))