combineresult: combining and formatting the individual PA results

In allenaigit/pathwayko: PathwayKO: An R package for knock-out pathway enrichment analysis

combining and formatting the individual PA results

Description

It yields _STATS.RData, summarizing and formatting the intermediate outputs such as true positive rates (TPR), true negative rates (TNR), false positive rates (FPR) and false negative rates (FNR), plus the Youden's best p-value threshold, sensitivity (TPR), specificity (TNR), accuracy, precision and recall.

Usage

combineresult()

Details

This function takes "*_SUM.RData" generated by pathwayko, combines them into a single object which can be further analyzed or plotted. All "_SUM" data should be analyzed by the same sets of PA methods, if not by identical PA methods under identical parameters. (i.e. with same KEGG xmls, same criteria for choosing DE genes, etc)

Value

TRUE when successful, FALSE otherwise

allenaigit/pathwayko documentation built on Nov. 23, 2022, 5:43 p.m.