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

In ROntoTools: R Onto-Tools suite

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"))

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