fit.em {metaArray} | R Documentation |
Probability of expresison from mixture distribution for a single gene.
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
fit.em(x, cl = NULL, threshold=1e-04)
Arguments
x |
A numeric vector, especially expression values for a particular gene. |
cl |
A vector of 0s and 1s. Use 0 for normal phenotype and 1 for
non-normal phenotype. Note that this is the opposite of POE MCMC. Labelling
is the opposite in poe.mcmc (will soon be corrected). If
left blank, all samples will be labeled as normal phenotype. When
class information is provided, conditional estimation of the mixture
is applied and POE is estimated unconditionally. |
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 |
conv |
Convergence status of EM |
dec |
Detection of decreasing likelihood |
loc |
Signs of local maxima |
lik.rec |
Trajectory of likelihood during EM |
abnormal |
Overall sign of failure in EM by any of the three criteria above |
Author(s)
Debashis Ghosh <ghoshd@umich.edu>, Hyungwon Choi <hwchoi@umich.edu>
Examples
[Package
metaArray version 1.4.4
Index]