optimize2: optimize2

In hubentu/PAIRADISE: PAIRADISE: Paired analysis of differential isoform expression

Description

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

Usage

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

Arguments

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.

Value

The MLEs.

hubentu/PAIRADISE documentation built on Oct. 4, 2020, 4:27 a.m.