optimize1: optimize1
In PAIRADISE: PAIRADISE: Paired analysis of differential isoform expression

Used internally in PAIRADISE to compute the MLEs of delta, mu, sigma1, sigma2, sigma

optimize1(
  x,
  M,
  I1,
  S1,
  I2,
  S2,
  l.iI,
  l.iS,
  logit.psi1,
  logit.psi2,
  alpha,
  equal.variance = FALSE
)

`x`	Numeric vector such that x = (sigma1, sigma2, sigma, mu, delta) if equal.variance = FALSE, and x = (sigma1, sigma, mu, delta) if equal.variance = TRUE. sigma1, sigma2, sigma must be positive
`M`	Number of replicates for the current exon.
`I1`	Exon inclusion counts for group 1. Positive integers.
`S1`	Exon skipping counts for group 1. Positive integers.
`I2`	Exon inclusion counts for group 2. Positive integers.
`S2`	Exon skipping counts for group 2. Positive integers.
`l.iI`	Effective length of inclusion isoform. Positive integer.
`l.iS`	Effective length of skipping isoform. Positive integer.
`logit.psi1`	Numeric vector with values of logit psi1.
`logit.psi2`	Numeric vector with values of logit psi2.
`alpha`	Numeric vector with values of alpha.
`equal.variance`	Are the group variances assumed equal? Default value is FALSE.