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

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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.

Author
Yue Li
Date of publication
None
Maintainer
Yue Li <yueli@cs.toronto.edu>
License
GPL-2
Version
1.12.0
URLs

View on Bioconductor

Man pages

bsxfun.se
bsxfun with single expansion (real Matlab style) (Internal...
dot.ext
Elementwise dot product (modified dot function) (Internal...
getTargetScores
Compute targetScore of an overexpressed human microRNA
initialization
Initialization of latent variable assignments...
logmvgamma
Logarithmic multivariate Gamma function (Internal function)
logsumexp
Compute log(sum(exp(x),dim)) while avoiding numerical...
sort_components
Sort mixture components in increasing order of averaged means...
targetScore
Probabilistic score of genes being the targets of an...
TargetScore-package
TargetScore: Infer microRNA targets using...
vbgmm
Variational Bayesian Gaussian mixture model (VB-GMM)
vbound
Variational Lower Bound Evaluation
vexp
Variational-Expectation in VB-EM (Internal function)
vmax
Variational-Maximimization in VB-EM (Internal function)

Files in this package

TargetScore/DESCRIPTION
TargetScore/NAMESPACE
TargetScore/R
TargetScore/R/getTargetScores.R
TargetScore/R/targetScore.R
TargetScore/R/vbgmm.R
TargetScore/build
TargetScore/build/vignette.rds
TargetScore/inst
TargetScore/inst/CITATION
TargetScore/inst/NEWS
TargetScore/inst/doc
TargetScore/inst/doc/TargetScore.R
TargetScore/inst/doc/TargetScore.Rnw
TargetScore/inst/doc/TargetScore.pdf
TargetScore/inst/extdata
TargetScore/inst/extdata/realtestdata.RData
TargetScore/man
TargetScore/man/TargetScore-package.Rd
TargetScore/man/bsxfun.se.Rd
TargetScore/man/dot.ext.Rd
TargetScore/man/getTargetScores.Rd
TargetScore/man/initialization.Rd
TargetScore/man/logmvgamma.Rd
TargetScore/man/logsumexp.Rd
TargetScore/man/sort_components.Rd
TargetScore/man/targetScore.Rd
TargetScore/man/vbgmm.Rd
TargetScore/man/vbound.Rd
TargetScore/man/vexp.Rd
TargetScore/man/vmax.Rd
TargetScore/vignettes
TargetScore/vignettes/TargetScore.Rnw
TargetScore/vignettes/TargetScore.bib