gprege

Package: gprege
Version: 1.16.0
Date: 2013-10-08
Title: Gaussian Process Ranking and Estimation of Gene Expression
time-series
Authors@R: c(person(c("Alfredo"), "Kalaitzis", role =
c("aut","cre","trl"), email = "alkalait@gmail.com"))
Author: Alfredo Kalaitzis <alkalait@gmail.com>
Maintainer: Alfredo Kalaitzis <alkalait@gmail.com>
Depends: R (>= 2.8.0), gptk
Suggests: spam
Description: 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).
License: AGPL-3
BugReports: alkalait@gmail.com
Packaged: 2016-05-04 04:28:12 UTC; biocbuild
biocViews: Microarray, Preprocessing, DifferentialExpression,
TimeCourse
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'gprege' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gprege'
    finding HTML links ... done
    DellaGattaData                          html  
    compareROC                              html  
    demTp63Gp1                              html  
    exhaustivePlot                          html  
    gprege-package                          html  
    finding level-2 HTML links ... done

    gprege                                  html  
    rocStats                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gprege)
Making 'packages.html' ... done