Estimate confidence intervals

Source: R/profile-likelihood.R

Estimate confidence intervals

ciGene(parName, geneIndexes, pd, par, options, interval, confidence = 0.95)

ci(paramPath, pd, par, options, freeParams, interval, confidence = 0.95)

Arguments

parName

a character, e.g. "mu"
geneIndexes

a vector; corresponds to the indexes of genes, for which the confidence intervals must be computed
pd

a PulseData object
par

a result of the fitModel function
options

an option list used for the fitModel call; additional options can be specified:

  • jitter, a double (default: .1)

  • replicates, an integer number of repeating the optimisation from random points

  • absolute, a logical (default: FALSE); if FALSE, the likelihood value at the optimal point (i.e. par) is substracted from the returned value. In this case, the value of the returned function at the point par is 0.
interval

a vector of too numbers, define (min, max) allowed parameter values
confidence

confidence level for interval estimation
paramPath

a list with names and indexes in order to locate the parameter in the par argument (e.g. list("mu", 1) corresponds to the "mu" parameter value for the first gene, i.e. par[["mu"]][[1]].
freeParams

which parameters are optimised (i.e. not fixed); by default they are derived from the names of the boundaries

Value

  • ciGene: a data.frame with two columns (left, right) confidence boundaries in the order of geneIndexes;

  • ci: a vector of two numbers;