ROntoTools (version 2.0.0)

summary.pDisRes: Summarize the results of a primary dis-regulation (pDis) analysis

Description

Summarize the results of a primary dis-regulation (pDis) analysis

Usage

summary.pDisRes(object, ..., pathNames = NULL, totalpDis = TRUE, normalize = TRUE,  ppDis = TRUE, pORA = TRUE,  comb.pv = c("ppDis", "pORA"), comb.pv.func = compute.fisher, order.by = "pComb", adjust.method = "fdr")

Arguments

object

pDis analysis result object obtained using pDis

...

ignored

pathNames

named vector of pathway names; the names of the vector are the IDs of the pathways

totalpDis

boolean value indicating if the total primary dis-regulation should be computed

normalize

boolean value indicating if normalization with regards to the boostrap simulations should be performed on totalpDis

ppDis

boolean value indicating if the significance of the total primary dis-regulation 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

pDis

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
pDisRes <- pDis(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

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

kpn <- keggPathwayNames("hsa")

head(summary(pDisRes))

head(summary(pDisRes, pathNames = kpn, totalpDis = FALSE, 
            pORA = FALSE, comb.pv = NULL, order.by = "pDis"))