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TargetScore (version 1.10.0)

TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information

Description

Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

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Version

Version

1.10.0

License

GPL-2

Maintainer

Yue Li

Last Published

February 15th, 2017

Functions in TargetScore (1.10.0)

logmvgamma

Logarithmic multivariate Gamma function (Internal function)
vbound

Variational Lower Bound Evaluation
TargetScore-package

TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
getTargetScores

Compute targetScore of an overexpressed human microRNA
logsumexp

Compute log(sum(exp(x),dim)) while avoiding numerical underflow (Internal function)
dot.ext

Elementwise dot product (modified dot function) (Internal function)
sort_components

Sort mixture components in increasing order of averaged means (Internal function)
initialization

Initialization of latent variable assignments (responsibility) of the VB-GMM (Internal function)
bsxfun.se

bsxfun with single expansion (real Matlab style) (Internal function)
targetScore

Probabilistic score of genes being the targets of an overexpressed microRNA
vbgmm

Variational Bayesian Gaussian mixture model (VB-GMM)
vexp

Variational-Expectation in VB-EM (Internal function)
vmax

Variational-Maximimization in VB-EM (Internal function)