fit.em: Probability of expresison from mixture distribution for a...

Description Usage Arguments Value Author(s)

Description

This core function fits two-component normal-uniform mixture distribution, and extracts probability of over/under expression for all samples in all genes.

Usage

1
  fit.em(x, cl, threshold=1e-06)

Arguments

x

A numeric vector, especially expression values for a particular gene.

cl

A vector of 0s and 1s. Use 1 for normal phenotype and 0 for non-normal phenotype. Note that this is the opposite of POE MCMC. If all samples are of unknown phenotype or of the same one, give vector of zeros. When class information is provided, conditional estimation of the mixture is applied.

threshold

Criterion for convergence in likelihood

Value

expr

Estimated POE

a

Minimum (adjusted) of Raw Expression

b

Maximum (adjusted) of Raw Expression

sigmasq

Estimated variance of normal component

mu

Estimated mean of normal component

Pi

Probability that the gene is over/under expressed on average across the samples

lik.rec

Trajectory of likelihood during EM

Author(s)

Debashis Ghosh <[email protected]>, Hyungwon Choi <[email protected]>


metaArray documentation built on Nov. 1, 2018, 2:27 a.m.