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MutationTime.R

MutationTime.R is an R script to time somatic mutations relative to clonal and subclonal copy number states and calculate the relative timing of copy number gains. It has been used by the PCAWG consortium to calculate mutation times of 2,778 whole genome sequencing samples. http://dx.doi.org/10.1101/161562

MutationTime.R needs the following input objects

source("MutationTime.R")
vcf <- readVcf("myvcf.vcf") # Point mutations, needs info columns t_alt_count t_ref_count
bb <- GRanges(, major_cn= , minor_cn=, clonal_frequency=purity) # Copy number segments, needs columns  major_cn, minor_cn and clonal_frequency of each segment

To run MutationTime.R

mt <- mutationTime(vcf, bb)

Mutation Annotation

head(param$D)

Classify as basic clonal states

table(classifyMutations(mt$D))

Time of copy number gains

bb$timing_param <- mt$P
bbToTime(bb)

MutationTime.R output

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An R package to time somatic mutations

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