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.

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

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

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