summary.peRes {ROntoTools} | R Documentation

## Summarize the results of a Pathway-Express analysis

### Description

Summarize the results of a Pathway-Express analysis

### Usage

    summary.peRes(object, ..., pathNames = NULL, totalAcc = TRUE, totalPert = TRUE, normalize = TRUE,
     pPert = TRUE, pAcc = TRUE, pORA = TRUE,
     comb.pv = c("pPert", "pORA"), comb.pv.func = compute.fisher,
     order.by = "pComb", adjust.method = "fdr")

### Arguments

`object` | Pathways-Express result object obtained using `pe`
`...` | ignored
`pathNames` | named vector of pathway names; the names of the vector are the IDs of the pathways
`totalAcc` | boolean value indicating if the total accumulation should be computed
`totalPert` | boolean value indicating if the total perturbation should be computed
`normalize` | boolean value indicating if normalization with regards to the boostrap simulations should be performed on totalAcc and totalPert
`pPert` | boolean value indicating if the significance of the total perturbation in regards to the bootstrap permutations should be computed
`pAcc` | boolean value indicating if the significance of the total accumulation in regards to the bootstrap permutations should be computed
`pORA` | boolean value indicating if the over-represtation p-value should be computed
`comb.pv` | vector of the p-value names to be combine (any of the above p-values)
`comb.pv.func` | the function to combine the p-values; takes as input a vector of p-values and returns the combined p-value
`order.by` | the name of the p-value that is used to order the results
`adjust.method` | the name of the method to adjust the p-value (see p.adjust)

### See Also

`pe`

### 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
    peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

    # obtain summary of results
    head(summary(peRes))

    kpn <- keggPathwayNames("hsa")

    head(summary(peRes))

    head(summary(peRes, pathNames = kpn, totalAcc = FALSE, totalPert = FALSE,
                 pAcc = FALSE, pORA = FALSE, comb.pv = NULL, order.by = "pPert"))

[Package ROntoTools version 2.12.0 Index]