getGenes: Gets significant genes within a certain window of...

In jmarlab/pathVar: Methods to Find Pathways with Significantly Different Variability

Description

Gets significant genes within a certain window of variability.

Usage

getGenes(pvalue_results,pathway,window)

Arguments

pvalue_results	output of pathVarTwoSamplesCont step.
pathway	A pathway name.
window	A vector with a min and max range to specify the window of genes to grab with a certain level of variance.

Details

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.

Value

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.

Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Examples

# 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))

jmarlab/pathVar documentation built on May 23, 2019, 9:02 p.m.