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.

Author
Hande Topa [aut, cre], Antti Honkela [aut]
Date of publication
2016-10-27 17:40:22
Maintainer
Hande Topa <hande.topa@helsinki.fi>
License
MIT + file LICENSE
Version
0.1.1
URLs

View on CRAN

Man pages

bbgp_snpData
Obtaining counts data in the format of example snpData by...
bitseq_fitGPs
Fitting GP models for the BitSeq example
bitseq_plotGP
Plotting fitted GP models for the BitSeq example
bitseq_rnaSeqData
Obtaining data in the format of example RNAseqDATA by using...
bitseq_setPlot
Configuring the settings of the plots for the BitSeq example
constructModel
Constructing GP model with the specified kernels
createDatabase
Building SQLite database
fixedvarianceKernCompute
fixedvarianceKernCompute
fixedvarianceKernDiagCompute
fixedvarianceKernDiagCompute
fixedvarianceKernExpandParam
fixedvarianceKernExpandParam
fixedvarianceKernExtractParam
fixedvarianceKernExtractParam
fixedvarianceKernGradient
fixedvarianceKernGradient
fixedvarianceKernParamInit
fixedvarianceKernParamInit
get_bbgpMeanStd
Computing means and standard deviations for the BBGP (beta...
getColorVector
Extracting distinctive colors from RColorBrewer package
getModelKernParams
Getting the values of the kernel parameters of the GP model
getYlimits
Setting limits for the y-axis
GPrank-package
GPrank - Gaussian Process ranking of multiple time series
gpTest
Performing Gaussian process test
plotGP
Plotting fitted GP models
RNAseqDATA
Sample data obtained from example BitSeq output files
setInitParams
Initializing kernel parameters
snpData
Sample data for demonstrating the application of experimental...

Files in this package

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/gpTest.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/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/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/README.md
GPrank/MD5
GPrank/build
GPrank/build/vignette.rds
GPrank/DESCRIPTION
GPrank/man
GPrank/man/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