Man pages for gerstung-lab/MutationTimeR
Timing somatic point mutations and copy number gains

addMetadataToHeaderAdd sample metadata entries to the VCF header
bbToTimeConvert timing parameters into timing estimates
classifyMutationsClassify Mutations
computeMutCnCompute timing parameters
defineMcnStatesCompute possible Mutation copy number states
getAltCountGet alt alleles counts
getClusterPowerGet mutation cluster power from VCF metadata
getMetaEntryConvenience function to fetch info from metadata
getPloidyGet sample ploidy from VCF metadata
getPurityGet sample purity from VCF metadata
getSexGet donor sex from VCF metadata
getSubclonalArchitectureGet sample subclonal architecture from VCF metadata
getTumorDepthExtract tumour depth
getWGDstatusGet sample whole genome doubling status from VCF metadata
mtHeaderReturn header elements
mutationTimeCompute mutation time from copy number gains and point...
MutationTimeRTiming of point mutations and copy number gains from deep...
plotSamplePlot timing
readVcfRead a VCF file
refLengthsReference lengths for hg37d5
writeVcfWrite a VCF file
gerstung-lab/MutationTimeR documentation built on Oct. 20, 2018, 1:38 a.m.