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 |
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