gprege: Gaussian Process Ranking and Estimation of Gene Expression time-series

The gprege package implements the methodology described in Kalaitzis & Lawrence (2011) "A simple approach to ranking differentially expressed gene expression time-courses through Gaussian process regression". The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via ROC curves is performed against BATS (Angelini et.al, 2007). A detailed discussion of the ranking approach and dataset used can be found in the paper (http://www.biomedcentral.com/1471-2105/12/180).

Author
Alfredo Kalaitzis <alkalait@gmail.com>
Date of publication
None
Maintainer
Alfredo Kalaitzis <alkalait@gmail.com>
License
AGPL-3
Version
1.18.0
URLs

View on Bioconductor

Man pages

compareROC
Make ROC plots.
DellaGattaData
Fragment dataset of 13 time-point mouse microarray time...
demTp63Gp1
gprege on TP63 expression time-series.
DGdat_p63
BATS rankings (Angelini, 2007) Case 1: Delta error prior Case...
exhaustivePlot
Plot of the LML function by exhaustive search.
gprege
Gaussian process ranking and estimation of gene expression...
gprege-package
gprege - Gaussian Process Ranking and Estimation of Gene...
rocStats
Make ROC curve data.

Files in this package

gprege/DESCRIPTION
gprege/NAMESPACE
gprege/R
gprege/R/compareROC.R
gprege/R/demTp63Gp1.R
gprege/R/exhaustivePlot.R
gprege/R/gprege.R
gprege/R/rocStats.R
gprege/build
gprege/build/vignette.rds
gprege/data
gprege/data/DGdat_p63.RData
gprege/data/FragmentDellaGattaData.RData
gprege/data/FullDellaGattaData.RData
gprege/data/datalist
gprege/inst
gprege/inst/CITATION
gprege/inst/NEWS
gprege/inst/doc
gprege/inst/doc/gprege_quick.R
gprege/inst/doc/gprege_quick.Rnw
gprege/inst/doc/gprege_quick.bib
gprege/inst/doc/gprege_quick.pdf
gprege/man
gprege/man/DGdat_p63.Rd
gprege/man/DellaGattaData.Rd
gprege/man/compareROC.Rd
gprege/man/demTp63Gp1.Rd
gprege/man/exhaustivePlot.Rd
gprege/man/gprege-package.Rd
gprege/man/gprege.Rd
gprege/man/rocStats.Rd
gprege/vignettes
gprege/vignettes/gprege_quick.Rnw
gprege/vignettes/gprege_quick.bib