summary.pDisRes {ROntoTools} | R Documentation |
Summarize the results of a primary dis-regulation (pDis) analysis
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")
object |
pDis analysis result object obtained using |
... |
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) |
# 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"))