Issue about the CCF calculation formula

[WangYfly-NJMU]

Dear author,
The SVCFit tool has demonstrated greater efficiency in my usage, but I have noticed a discrepancy between the formula for calculating CCF in the preprint and the code. In the preprint, CCF = purity * SVCF, but in the Figure1.Rmd you provided, the formula for calculating CCF is SVCF / purity. Which formula should we choose? Referring to the formula MCF/purity = CCF, I think SVCF/purity is correct. Do you agree?

mix3 <- mix %>%
  filter(!sample %in% c("4m","5m"))%>%
  rowwise()%>%
  mutate(bmr = as.integer(gsub("3m(\\d)(\\d)", "\\1", sample))/10,
         gmr = as.integer(gsub("3m(\\d)(\\d)", "\\2", sample))/10,
         purity = 0.49*bmr+0.46*gmr,
         true_row = ifelse(any(abs(POS-true$POS)<6),which(abs(POS-true$POS)<6), NA),
         clone= true$clone[true_row],
         ccf = ifelse(clone == "bM", bmr,
                      ifelse(clone == "gM", gmr, 1)),
         my_ccf = svcf/purity,
         my_ccf = ifelse(my_ccf > 1, 1, my_ccf),
         error = ccf-my_ccf)%>%
  ungroup()%>%
  distinct(ID, .keep_all = T)%>%
  filter(!is.na(clone))%>%
  select(sample, ccf, svcf, my_ccf, error, clone)

Best wishes.
Wang Yifan

[RachelKarchin]

Hi Wang,

Sorry for our delayed response. We have a new version of SVCFit that we are releasing this week.

You are correct. The preprint had a typo. Thanks so much for catching that.
CCF is SVCF / purity
per the code in Figure1.Rmd

Best