ROntoTools (version 2.0.0)

summary.peRes: 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"))