Man pages for gerstung-lab/MutationTimeR
Timing somatic point mutations and copy number gains
| addMetadataToHeader | Add sample metadata entries to the VCF header |
| addMutTime | Add mutation timing information to vcf object |
| classifyMutations | Classify Mutations |
| classWgd | Heuristic to classify WGD based on CN profile |
| getAltCount | Get alt alleles counts |
| getClusterPower | Get mutation cluster power from VCF metadata |
| getHomozygousity | Extract the average homozygousity from copy number |
| getMetaEntry | Convenience function to fetch info from metadata |
| getPloidy | Extract the average ploidy from copy number |
| getPurity | Get sample purity from VCF metadata |
| getSex | Get donor sex from VCF metadata |
| getSubclonalArchitecture | Get sample subclonal architecture from VCF metadata |
| getTumorDepth | Extract tumour depth |
| getWGDstatus | Get sample whole genome doubling status from VCF metadata |
| mutationTime | Compute mutation time from copy number gains and point... |
| MutationTimeR | Timing of point mutations and copy number gains from deep... |
| plotSample | Plot timing |
| readVcf | Read a VCF file |
| refLengths | Reference lengths for hg37d5 |
| writeVcf | Write a VCF file |
