| Function | Description |
| apEX | Example data set for apComplex package |
| bhmaxSubgraph | Find maximal BH-complete subgraph |
| findComplexes | Estimate a Protein Complex Membership Graph (PCMG) using protein complex comembership data from AP-MS technology |
| HMSPCI | High-Throughput Mass Spectromic Protein Complex Identification (HMS-PCI) Data from Ho, et al. (2002) |
| LCdelta | Computes change in LxC measure |
| MBMEcHMSPCI | HMSPCI data complex estimates |
| MBMEcTAP | TAP data complex estimates |
| mergeComplexes | Iteratively combine columns in initial PCMG estimate |
| reduceMat | Remove matrix columns |
| sortComplexes | Sort complex estimates |
| TAP | Tandem Affinity Purification (TAP) Data from Gavin et al. (2002) |
| vecInMat | Vector in Matrix |
| yTAP | yTAP Complexes published Gavin, et al. (2002). |