View source: R/LLHSpectrumNegBinom.R
LLHSpectrumNegBinom | R Documentation |
Likelihood that 1 observed spectrum was generated from a vector of expected mutation counts.
LLHSpectrumNegBinom(spectrum, expected.counts, nbinom.size, verbose = FALSE)
spectrum |
An observed spectrum (a numeric vector) |
expected.counts |
A vector of (integer) expected mutation counts, one
expected count for each mutation type. We want to know the
likelihood that this model generated the observed
spectrum, assuming each mutational types generates counts according to
a negative binomial distribution with
the given |
nbinom.size |
The dispersion parameter for the negative
binomial distribution; smaller is more dispersed.
See |
verbose |
If |
log(likelihood(spectrum | expected.counts))
, or,
in more detail,
the sum of the negative binomial likelihoods
that each each element of the
spectrum (i.e., the count for each mutation type e.g. ACT > AAT)
was generated from the expected count for that mutation type.
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