plot,peRes,missing-method {ROntoTools} | R Documentation |
Display a two-way plot using two of the p-values from the Pathway-Express analysis.
## S4 method for signature 'peRes,missing' plot(x, y, ..., comb.pv.func = compute.fisher, adjust.method = "fdr", threshold = 0.05, eps = 1e-06) ## S4 method for signature 'peRes,character' plot(x, y, ..., comb.pv.func = compute.fisher, adjust.method = "fdr", threshold = 0.05, eps = 1e-06)
x |
an object of type |
y |
vector of two p-values names to be combined using |
... |
Arguments to be passed to methods, such as |
comb.pv.func |
the function to combine the p-values - takes as input a vector of p-values
and returns the combined p-value (default: |
adjust.method |
the name of the method to adjust the p-value (see |
threshold |
corrected p-value threshold |
eps |
any value smaller than this will be considered as |
Calin Voichita and Sorin Draghici
pe
, summary.peRes
, plot,pePathway,missing-method
# load experiment load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools")) fc <- top$logFC[top$adj.P.Val <= .01] names(fc) <- top$entrez[top$adj.P.Val <= .01] ref <- top$entrez # load the set of pathways kpg <- keggPathwayGraphs("hsa") kpg <- setEdgeWeights(kpg) kpg <- setNodeWeights(kpg, defaultWeight = 1) # perform the pathway analysis (for more accurate results use nboot = 2000) peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE) plot(peRes) plot(peRes, c("pPert","pORA"), comb.pv.func = compute.normalInv, threshold = .01)