GPrank: Gaussian Process Ranking of Multiple Time Series

Implements a Gaussian process (GP)-based ranking method which can be used to rank multiple time series according to their temporal activity levels. An example is the case when expression levels of all genes are measured over a time course and the main concern is to identify the most active genes, i.e. genes which show significant non-random variation in their expression levels. This is achieved by computing Bayes factors for each time series by comparing the marginal likelihoods under time-dependent and time-independent GP models. Additional variance information from pre-processing of the observations is incorporated into the GP models, which makes the ranking more robust against model overfitting. The package supports exporting the results to 'tigreBrowser' for visualisation, filtering or ranking.

Install the latest version of this package by entering the following in R:
install.packages("GPrank")
AuthorHande Topa [aut, cre], Antti Honkela [aut]
Date of publication2016-12-21 17:02:00
MaintainerHande Topa <hande.topa@helsinki.fi>
LicenseMIT + file LICENSE
Version0.1.2
https://github.com/PROBIC/GPrank

View on CRAN

Functions

apply_gpTest Man page
bbgp_snpData Man page
bitseq_fitGPs Man page
bitseq_plotGP Man page
bitseq_rnaSeqData Man page
bitseq_setPlot Man page
constructModel Man page
createDatabase Man page
fixedvarianceKernCompute Man page
fixedvarianceKernDiagCompute Man page
fixedvarianceKernExpandParam Man page
fixedvarianceKernExtractParam Man page
fixedvarianceKernGradient Man page
fixedvarianceKernParamInit Man page
get_bbgpMeanStd Man page
getColorVector Man page
getModelKernParams Man page
getYlimits Man page
GPrank-package Man page
plotGP Man page
RNAseqDATA Man page
setInitParams Man page
snpData Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/doc/vignette.R
NAMESPACE
data
data/RNAseqDATA.RData
data/snpData.RData
R
R/getColorVector.R R/fixedvarianceKernGradient.R R/setInitParams.R R/bitseq_setPlot.R R/fixedvarianceKernExtractParam.R R/fixedvarianceKernCompute.R R/bitseq_rnaSeqData.R R/bitseq_fitGPs.R R/RNAseqDATA-data.R R/apply_gpTest.R R/constructModel.R R/bbgp_snpData.R R/createDatabase.R R/bitseq_plotGP.R R/getYlimits.R R/fixedvarianceKernParamInit.R R/getModelKernParams.R R/plotGP.R R/fixedvarianceKernExpandParam.R R/fixedvarianceKernDiagCompute.R R/GPrank-package.R R/get_bbgpMeanStd.R R/snpData-data.R
vignettes
vignettes/figures
vignettes/figures/geneB_GP.png
vignettes/figures/geneA_GP.png
vignettes/vignette.Rnw
vignettes/t0020.rpkm
vignettes/natbib.bst
vignettes/t0040.rpkm
vignettes/t0000.rpkm
vignettes/example_tr
vignettes/t0640.rpkm
vignettes/t0160.rpkm
vignettes/t0080.rpkm
vignettes/t1280.rpkm
vignettes/natbib.sty
vignettes/GPrank_refs.bib
vignettes/t0010.rpkm
vignettes/t0005.rpkm
vignettes/t0320.rpkm
vignettes/sampleCountsData
MD5
build
build/vignette.rds
DESCRIPTION
man
man/apply_gpTest.Rd man/bitseq_fitGPs.Rd man/bitseq_rnaSeqData.Rd man/fixedvarianceKernParamInit.Rd man/RNAseqDATA.Rd man/constructModel.Rd man/fixedvarianceKernExpandParam.Rd man/fixedvarianceKernDiagCompute.Rd man/bitseq_setPlot.Rd man/getYlimits.Rd man/fixedvarianceKernCompute.Rd man/snpData.Rd man/getModelKernParams.Rd man/createDatabase.Rd man/plotGP.Rd man/get_bbgpMeanStd.Rd man/fixedvarianceKernGradient.Rd man/setInitParams.Rd man/bitseq_plotGP.Rd man/bbgp_snpData.Rd man/GPrank-package.Rd man/fixedvarianceKernExtractParam.Rd man/getColorVector.Rd
LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.