plot.peRes-methods: Plot Pathway-Express result

In ROntoTools: R Onto-Tools suite

Description

Display a two-way plot using two of the p-values from the Pathway-Express analysis.

Usage

## 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)

Arguments

x	an object of type peRes-class
y	vector of two p-values names to be combined using comb.pv.func (default: c("pAcc", "pORA")).
...	Arguments to be passed to methods, such as par.
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: compute.fisher).
adjust.method	the name of the method to adjust the p-value (see p.adjust)
threshold	corrected p-value threshold
eps	any value smaller than this will be considered as eps (default: 1e-6).

Author(s)

Calin Voichita and Sorin Draghici

See Also

pe, summary.peRes, plot,pePathway,missing-method

Examples

# 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)

ROntoTools documentation built on Nov. 8, 2020, 7:41 p.m.