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Table 1 Expanded Q matrix for ternary data

From: Comments on the model parameters in “SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models”

 

0/-

0/0

0/1

1/-

1/1

0/-

0

NA

NA

NA

NA

0/0

λ l

-1 - λl

1

NA

NA

0/1

\(\frac {\lambda _{l}}{2}\)

\(\frac {\lambda _{d}}{2}\)

−(λd+λl)

\(\frac {\lambda _{l}}{2}\)

\(\frac {\lambda _{d}}{2}\)

1/-

NA

NA

NA

0

NA

1/1

NA

NA

λ d

λ l

λlλd

  1. Q(i,j) denotes transition from state i to state j. The transitions for which the entry is ‘NA’, are not allowed. In particular, we do not allow the transitions 0/- → 1/- or 1/- →0/- as a reflection of a simplifying assumption that a recurrent point mutation and deletion/LOH occurring at the same site is a very rare event. Furthermore, we do not model copy number gain.