plot,peRes,missing-method {ROntoTools} | R Documentation

## Plot Pathway-Express result

### 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)

[Package ROntoTools version 2.18.0 Index]