optimize2: optimize2
In PAIRADISE: PAIRADISE: Paired analysis of differential isoform expression

Used internally in PAIRADISE to compute the MLEs of logit(psi1), logit(psi2), alpha

1	optimize2(x, k, I1, S1, I2, S2, l.iI, l.iS, delta, mu, s1, s2, s)

`x`	Numeric vector such that x = (logit(psi1), logit(psi2), alpha)
`k`	Index representing current replicate number.
`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.
`delta`	Parameter delta.
`mu`	Parameter mu.
`s1`	Group 1 standard deviation. Positive number.
`s2`	Group 2 standard deviation. Positive number.
`s`	Overall standard deviation. Positive number.