optimize1: optimize1

Description Usage Arguments Value

View source: R/optimize1.R

Description

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

Usage

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

Arguments

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.

Value

The MLEs.


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