pRoloc: A unifying bioinformatics framework for spatial proteomics

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This package implements pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation.

Author
Laurent Gatto and Lisa M. Breckels with contributions from Thomas Burger and Samuel Wieczorek
Date of publication
None
Maintainer
Laurent Gatto <lg390@cam.ac.uk>
License
GPL-2
Version
1.14.5
URLs

View on Bioconductor

Man pages

addGoAnnotations
Add GO annotations
addLegend
Adds a legend
addMarkers
Adds markers to the data
AnnotationParams-class
Class '"AnnotationParams"'
checkFeatureNamesOverlap
Check feature names overlap
checkFvarOverlap
Compare a feature variable overlap
chi2-methods
The PCP 'chi square' method
classWeights
Calculate class weights
clustDist
Pairwise Distance Computation for Protein Information Sets
ClustDist-class
Class '"ClustDist"'
ClustDistList-class
Storing multiple ClustDist instances
defunct
pRoloc Deprecated and Defunct
empPvalues
Estimate empirical p-values for Chi^2 protein correlations.
exprsToRatios-methods
Calculate all ratio pairs
fDataToUnknown
Update a feature variable
filterBinMSnSet
Filter a binary MSnSet
filterMaxMarkers
Removes class/annotation information from a matrix of...
filterMinMarkers
Removes class/annotation information from a matrix of...
filterZeroCols
Remove 0 columns/rows
GenRegRes-class
Class '"GenRegRes"' and '"ThetaRegRes"'
getGOFromFeatures
Retrieve GO terms for feature names
getMarkerClasses
Returns the organelle classes in an 'MSnSet'
getMarkers
Get the organelle markers in an 'MSnSet'
getNormDist
Extract Distances from a '"ClustDistList"' object
getPredictions
Returns the predictions in an 'MSnSet'
getStockcol
Manage default colours and point characters
goIdToTerm
Convert GO ids to/from terms
highlightOnPlot
Highlight features of interest on a spatial proteomics plot
knnClassification
knn classification
knnOptimisation
knn parameter optimisation
knntlClassification
knn transfer learning classification
knntlOptimisation
theta parameter optimisation
ksvmClassification
ksvm classification
ksvmOptimisation
ksvm parameter optimisation
lopims
A complete LOPIMS pipeline
makeGoSet
Creates a GO feature 'MSnSet'
markerMSnSet
Extract marker/unknown subsets
markers
Create a marker vector or matrix.
MartInstance-class
Class '"MartInstance"'
minMarkers
Creates a reduced marker variable
MLearn-methods
The 'MLearn' interface for machine learning
move2Ds
Displays a spatial proteomics animation
mrkHClust
Draw a dendrogram of subcellular clusters
nbClassification
nb classification
nbOptimisation
nb paramter optimisation
nndist-methods
Nearest neighbour distances
nnetClassification
nnet classification
nnetOptimisation
nnet parameter optimisation
orderGoAnnotations
Orders annotation information
orgQuants
Returns organelle-specific quantile scores
perTurboClassification
perTurbo classification
perTurboOptimisation
PerTurbo parameter optimisation
phenoDisco
Runs the 'phenoDisco' algorithm.
plot2D
Plot organelle assignment data and results.
plot2Ds
Draw 2 data sets on one PCA plot
plotDist
Plots the distribution of features across fractions
plsdaClassification
plsda classification
plsdaOptimisation
plsda parameter optimisation
pRolocmarkers
Organelle markers
pRoloc-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("pRoloc")}
QSep-class
Quantify resolution of a spatial proteomics experiment
rfClassification
rf classification
rfOptimisation
svm parameter optimisation
sampleMSnSet
Extract a stratified sample of an 'MSnSet'
showGOEvidenceCodes
GO Evidence Codes
SpatProtVis-class
Class 'SpatProtVis'
subsetMarkers
Subsets markers
svmClassification
svm classification
svmOptimisation
svm parameter optimisation
testMarkers
Tests marker class sizes
testMSnSet
Create a stratified 'test' 'MSnSet'
thetas
Draw matrix of thetas to test
undocumented
Undocumented/unexported entries
zerosInBinMSnSet
Compute the number of non-zero values in each marker classes

Files in this package

pRoloc/CONDUCT.md
pRoloc/DESCRIPTION
pRoloc/NAMESPACE
pRoloc/NEWS
pRoloc/R
pRoloc/R/AllGenerics.R
pRoloc/R/MLInterfaces.R
pRoloc/R/MSnSet.R
pRoloc/R/MartInterface.R
pRoloc/R/annotation.R
pRoloc/R/belief.R
pRoloc/R/chi2.R
pRoloc/R/clusterdist-framework.R
pRoloc/R/clusterdist-functions.R
pRoloc/R/clustering-framework.R
pRoloc/R/clustering-kmeans.R
pRoloc/R/distances.R
pRoloc/R/dynamics.R
pRoloc/R/environment.R
pRoloc/R/go.R
pRoloc/R/goannotations.R
pRoloc/R/goenv.R
pRoloc/R/hclust.R
pRoloc/R/lopims.R
pRoloc/R/machinelearning-framework-theta.R
pRoloc/R/machinelearning-framework.R
pRoloc/R/machinelearning-functions-PerTurbo.R
pRoloc/R/machinelearning-functions-knn.R
pRoloc/R/machinelearning-functions-knntl.R
pRoloc/R/machinelearning-functions-ksvm.R
pRoloc/R/machinelearning-functions-nb.R
pRoloc/R/machinelearning-functions-nnet.R
pRoloc/R/machinelearning-functions-plsda.R
pRoloc/R/machinelearning-functions-rf.R
pRoloc/R/machinelearning-functions-svm.R
pRoloc/R/machinelearning-utils.R
pRoloc/R/makeGoSet.R
pRoloc/R/markers.R
pRoloc/R/pRolocmarkers.R
pRoloc/R/perTurbo-algorithm.R
pRoloc/R/phenodisco.R
pRoloc/R/plotting.R
pRoloc/R/plotting2.R
pRoloc/R/plotting3.R
pRoloc/R/qsep.R
pRoloc/R/utils.R
pRoloc/R/vis.R
pRoloc/R/zzz.R
pRoloc/README
pRoloc/build
pRoloc/build/partial.rdb
pRoloc/build/vignette.rds
pRoloc/data
pRoloc/data/andy2011params.rda
pRoloc/data/dunkley2006params.rda
pRoloc/inst
pRoloc/inst/CITATION
pRoloc/inst/doc
pRoloc/inst/doc/HUPO_2011_poster.R
pRoloc/inst/doc/HUPO_2011_poster.Rnw
pRoloc/inst/doc/HUPO_2011_poster.pdf
pRoloc/inst/doc/HUPO_2014_poster.R
pRoloc/inst/doc/HUPO_2014_poster.Rnw
pRoloc/inst/doc/HUPO_2014_poster.pdf
pRoloc/inst/doc/pRoloc-goannotations.R
pRoloc/inst/doc/pRoloc-goannotations.Rmd
pRoloc/inst/doc/pRoloc-goannotations.html
pRoloc/inst/doc/pRoloc-ml.Rnw
pRoloc/inst/doc/pRoloc-ml.pdf
pRoloc/inst/doc/pRoloc-transfer-learning.R
pRoloc/inst/doc/pRoloc-transfer-learning.Rnw
pRoloc/inst/doc/pRoloc-transfer-learning.pdf
pRoloc/inst/doc/pRoloc-tutorial.Rnw
pRoloc/inst/doc/pRoloc-tutorial.pdf
pRoloc/inst/extdata
pRoloc/inst/extdata/dunkley2006pdunittest1.rda
pRoloc/inst/extdata/dunkley2006pdunittest2.rda
pRoloc/inst/extdata/dunkley2006pdunittest_20140408.rda
pRoloc/inst/extdata/marker_atha.rds
pRoloc/inst/extdata/marker_dmel.rds
pRoloc/inst/extdata/marker_ggal.rds
pRoloc/inst/extdata/marker_hsap.rds
pRoloc/inst/extdata/marker_mmus.rds
pRoloc/inst/extdata/marker_scer_sgd.rds
pRoloc/inst/extdata/marker_scer_uniprot.rds
pRoloc/inst/extdata/mil.rds
pRoloc/inst/extdata/params.rda
pRoloc/inst/extdata/params2.rda
pRoloc/inst/extdata/pdres.rda
pRoloc/inst/figs
pRoloc/inst/figs/plot2D-hexbin.png
pRoloc/inst/figs/plot2D-lda.png
pRoloc/inst/figs/plot2D-null-black.png
pRoloc/inst/figs/plot2D-null-cex.png
pRoloc/inst/figs/plot2D-null-pch-black.png
pRoloc/inst/figs/plot2D-null-pch.png
pRoloc/inst/figs/plot2D-null.png
pRoloc/inst/figs/plot2D-scree.png
pRoloc/inst/figs/plot2D.png
pRoloc/inst/scripts
pRoloc/inst/scripts/biomart.R
pRoloc/inst/scripts/dynamics.R
pRoloc/inst/scripts/test_pd.R
pRoloc/man
pRoloc/man/AnnotationParams-class.Rd
pRoloc/man/ClustDist-class.Rd
pRoloc/man/ClustDistList-class.Rd
pRoloc/man/GenRegRes-class.Rd
pRoloc/man/MLearn-methods.Rd
pRoloc/man/MartInstance-class.Rd
pRoloc/man/QSep-class.Rd
pRoloc/man/SpatProtVis-class.Rd
pRoloc/man/addGoAnnotations.Rd
pRoloc/man/addLegend.Rd
pRoloc/man/addMarkers.Rd
pRoloc/man/checkFeatureNamesOverlap.Rd
pRoloc/man/checkFvarOverlap.Rd
pRoloc/man/chi2-methods.Rd
pRoloc/man/classWeights.Rd
pRoloc/man/clustDist.Rd
pRoloc/man/defunct.Rd
pRoloc/man/empPvalues.Rd
pRoloc/man/exprsToRatios-methods.Rd
pRoloc/man/fDataToUnknown.Rd
pRoloc/man/filterBinMSnSet.Rd
pRoloc/man/filterMaxMarkers.Rd
pRoloc/man/filterMinMarkers.Rd
pRoloc/man/filterZeroCols.Rd
pRoloc/man/getGOFromFeatures.Rd
pRoloc/man/getMarkerClasses.Rd
pRoloc/man/getMarkers.Rd
pRoloc/man/getNormDist.Rd
pRoloc/man/getPredictions.Rd
pRoloc/man/getStockcol.Rd
pRoloc/man/goIdToTerm.Rd
pRoloc/man/highlightOnPlot.Rd
pRoloc/man/knnClassification.Rd
pRoloc/man/knnOptimisation.Rd
pRoloc/man/knntlClassification.Rd
pRoloc/man/knntlOptimisation.Rd
pRoloc/man/ksvmClassification.Rd
pRoloc/man/ksvmOptimisation.Rd
pRoloc/man/lopims.Rd
pRoloc/man/makeGoSet.Rd
pRoloc/man/markerMSnSet.Rd
pRoloc/man/markers.Rd
pRoloc/man/minMarkers.Rd
pRoloc/man/move2Ds.Rd
pRoloc/man/mrkHClust.Rd
pRoloc/man/nbClassification.Rd
pRoloc/man/nbOptimisation.Rd
pRoloc/man/nndist-methods.Rd
pRoloc/man/nnetClassification.Rd
pRoloc/man/nnetOptimisation.Rd
pRoloc/man/orderGoAnnotations.Rd
pRoloc/man/orgQuants.Rd
pRoloc/man/pRoloc-package.Rd
pRoloc/man/pRolocmarkers.Rd
pRoloc/man/perTurboClassification.Rd
pRoloc/man/perTurboOptimisation.Rd
pRoloc/man/phenoDisco.Rd
pRoloc/man/plot2D.Rd
pRoloc/man/plot2Ds.Rd
pRoloc/man/plotDist.Rd
pRoloc/man/plsdaClassification.Rd
pRoloc/man/plsdaOptimisation.Rd
pRoloc/man/rfClassification.Rd
pRoloc/man/rfOptimisation.Rd
pRoloc/man/sampleMSnSet.Rd
pRoloc/man/showGOEvidenceCodes.Rd
pRoloc/man/subsetMarkers.Rd
pRoloc/man/svmClassification.Rd
pRoloc/man/svmOptimisation.Rd
pRoloc/man/testMSnSet.Rd
pRoloc/man/testMarkers.Rd
pRoloc/man/thetas.Rd
pRoloc/man/undocumented.Rd
pRoloc/man/zerosInBinMSnSet.Rd
pRoloc/src
pRoloc/src/Makevars
pRoloc/src/Makevars.win
pRoloc/src/pRoloc.cpp
pRoloc/tests
pRoloc/tests/testthat
pRoloc/tests/testthat.R
pRoloc/tests/testthat/test_SpatProtVis.R
pRoloc/tests/testthat/test_annotation.R
pRoloc/tests/testthat/test_classWeights.R
pRoloc/tests/testthat/test_clustDist.R
pRoloc/tests/testthat/test_data.R
pRoloc/tests/testthat/test_dist.R
pRoloc/tests/testthat/test_go.R
pRoloc/tests/testthat/test_goannotations.R
pRoloc/tests/testthat/test_markers.R
pRoloc/tests/testthat/test_ml.R
pRoloc/tests/testthat/test_plot2D.R
pRoloc/tests/testthat/test_qsep.R
pRoloc/tests/testthat/test_theta.R
pRoloc/tests/testthat/test_utils.R
pRoloc/vignettes
pRoloc/vignettes/Bugs.tex
pRoloc/vignettes/Figures
pRoloc/vignettes/Figures/F1boxplots.pdf
pRoloc/vignettes/Figures/ISL-2_16.pdf
pRoloc/vignettes/Figures/ISL-2_17.pdf
pRoloc/vignettes/Figures/Screenshot_PCA2.png
pRoloc/vignettes/Figures/ap1.png
pRoloc/vignettes/Figures/ap2.png
pRoloc/vignettes/Figures/bubble-andy.pdf
pRoloc/vignettes/Figures/knnboundaries.R
pRoloc/vignettes/Figures/knnboundaries.pdf
pRoloc/vignettes/Figures/msnset.ditaa
pRoloc/vignettes/Figures/msnset.png
pRoloc/vignettes/Figures/organelle_proteomics.ditaa
pRoloc/vignettes/Figures/organelle_proteomics.png
pRoloc/vignettes/Figures/phenodisco.pdf
pRoloc/vignettes/Figures/phenodisco.tex
pRoloc/vignettes/Figures/plot3D.png
pRoloc/vignettes/Foreword.tex
pRoloc/vignettes/HUPO_2011_poster.Rnw
pRoloc/vignettes/HUPO_2014_poster.Rnw
pRoloc/vignettes/HUPO_2014_poster.tex
pRoloc/vignettes/Makefile
pRoloc/vignettes/figure
pRoloc/vignettes/pRoloc-goannotations.Rmd
pRoloc/vignettes/pRoloc-ml.Rnw
pRoloc/vignettes/pRoloc-transfer-learning.Rnw
pRoloc/vignettes/pRoloc-transfer-learning.tex
pRoloc/vignettes/pRoloc-tutorial.Rnw
pRoloc/vignettes/pRoloc.bib
pRoloc/vignettes/vigsrc
pRoloc/vignettes/vigsrc/HUPO_2011_poster.pdf
pRoloc/vignettes/vigsrc/HUPO_2014_poster.pdf