Man pages for qingjian1991/MPTevol
Clonal Evolutionary History and Metastatic Routines Analysis for Multiple Primary Tumors
| calKaKs | calKaKs calculates the Ka/Ks of each group |
| calPropDriver | calPropDriver calculates the proportions of driver mutation... |
| calRoutines | calRoutines calculates the H index and JSI index according to... |
| getClinSites | getClinSites captures the clinical targetable sites of oncokb... |
| getKaKs | getKaKs compares Ka/Ks between different groups |
| inferClonalTrees | inferClonalTrees |
| maf2variants | maf2variants |
| MPTevol-package | MPTevol: Clonal Evolutionary History and Metastatic Routines... |
| pipe | Pipe operator |
| plotCNA | plotCNA |
| plotCNAProfile | Visualize CNA profile |
| plotCNAtree | plotCNAtree plots phylogenetic trees of CNAs |
| plotMutTree | plotMutTree plots phylogenetic tree of mutations |
| plotVafCluster | plotVafCluster |
| readCNAProfile | Read CNA Profiles |
| readMaf | readMaf |
| Seg-class | Segment Class |
| set.colors | Color setting |
| splitSegment | Split the segment regions into several parts |
| tree2timescape | tree2timescape |
| viewTrees | Visualize the trees |
| write.fasta | write.fasta |
