summary.peRes: Summarize the results of a Pathway-Express analysis

In ROntoTools: R Onto-Tools suite

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"))

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