Man pages for allenaigit/pathwayko
PathwayKO: An R package for knock-out pathway enrichment analysis
| combineresult | combining and formatting the individual PA results |
| evidenceplot | generating two-dimensional evidence plot |
| filtertrue | extracting the list of true positive KO KEGG pathways |
| highedges | calculating edge scores, determining the change-point and... |
| makeSPIAdata | parsing KEGG xmls ready for pathway enrichment analysis |
| pathwayko | performing the KO pathway enrichment analysis on single... |
| pathwayko_batch | batch-performing the KO pathway enrichment analysis on... |
| pathwayko_demo | for pathwayko_demo on 10 KO GEO datasets |
| pathwayview | rendering the true positive KO KEGG pathways by the up- and... |
| preprocess | preprocessing GSE data from CEL files and series matrix file |
| roctest | conducting ROC-curve based statistics analysis |
| violinplot | generating violinplots based on the combined PA results |
| wilcoxtest | performing pairwise comparisons on the PA results |
