pRoloc: A unifying bioinformatics framework for spatial proteomics
Version 1.16.1

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

Browse man pages Browse package API and functions Browse package files

AuthorLaurent Gatto and Lisa M. Breckels with contributions from Thomas Burger and Samuel Wieczorek
Bioconductor views Classification Clustering MassSpectrometry Proteomics QualityControl
Date of publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseGPL-2
Version1.16.1
URL https://github.com/lgatto/pRoloc
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pRoloc")

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
mrkConsProfiles: Marker consensus profiles
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: A unifying bioinformatics framework for spatial proteomics
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

Functions

AnnotationParams Man page Man page
AnnotationParams-class Man page
BUG_splitTh Source code
ClustDist Man page
ClustDist-class Man page
ClustDistList Man page Source code
ClustDistList-class Man page
GenRegRes Man page
GenRegRes-class Man page
MLearn,formula,MSnSet,clusteringSchema,missing-method Man page
MLearn,formula,MSnSet,learnerSchema,numeric-method Man page
MLearn,formula,MSnSet,learnerSchema,xvalSpec-method Man page
MLearnMSnSet Man page
MSnSetMLean Man page
MartInstance Man page Source code
MartInstance-class Man page
MartInstanceList Man page Source code
MartInstanceList-class Man page
QSep Man page Source code
QSep-class Man page
SpatProtVis Man page Source code
SpatProtVis-class Man page
ThetaRegRes Man page
ThetaRegRes-class Man page
[,ClustDistList,ANY,ANY,ANY-method Man page
[,ClustDistList,ANY,missing,missing-method Man page
[,MartInstanceList,ANY,ANY,ANY-method Man page
[,MartInstanceList,ANY,ANY-method Man page
[,MartInstanceList-method Man page
[[,ClustDistList,ANY,ANY-method Man page
[[,ClustDistList,ANY,missing-method Man page
[[,MartInstanceList,ANY,ANY-method Man page
[[,MartInstanceList-method Man page
addConvexHulls Source code
addGoAnnotations Man page Source code
addLegend Man page Source code
addMarkers Man page Source code
andy2011params Man page
anyUnknown Source code
as.data.frame.MartInstance Man page Source code
as.data.frame.MartInstanceList Man page Source code
bel Source code
checkAttr0 Source code
checkAttrX Source code
checkFeatureNames Source code
checkFeatureNamesOverlap Man page Source code
checkFvarOverlap Man page Source code
checkNumbers Source code
checkSortedFeatureNames Source code
chi2 Man page
chi2,matrix,matrix-method Man page
chi2,matrix,numeric-method Man page
chi2,numeric,matrix-method Man page
chi2,numeric,numeric-method Man page
chi2-methods Man page
chooseAttributesX Source code
class::QSep Man page
class:AnnotationParams Man page
class:ClustDist Man page
class:ClustDistList Man page
class:GenRegRes Man page
class:SpatProtVis Man page
class:ThetaRegRes Man page
classWeights Man page Source code
classify Source code
clustDist Man page Source code
clustdists Source code
clusterDistK Source code
col1 Man page Source code
col2 Man page Source code
combineParams Source code
combineThetaRegRes Man page Source code
constructDataSet Source code
controlParameters Source code
createPartitions Source code
data1 Man page Source code
data2 Man page Source code
diffscore Source code
diffscores Source code
difftorand Source code
dunkley2006params Man page
empPvalues Man page Source code
estimateVariance Source code
exprsToRatios Man page
exprsToRatios,MSnSet-method Man page
exprsToRatios-methods Man page
f1Count Man page
f1Count,GenRegRes-method Man page
f1Count,ThetaRegRes-method Man page
fDataToUnknown Man page Source code
favourPrimary Man page Source code
filterAttrs Man page Source code
filterBinMSnSet Man page Source code
filterMaxMarkers Man page Source code
filterMinMarkers Man page Source code
filterZeroCols Man page Source code
filterZeroRows Man page Source code
flipGoTermId Man page Source code
getAnnotationParams Man page Source code
getAttributesOfInterest0 Source code
getAttributesOfInterestX Source code
getBestParams Source code
getClusterInfo Source code
getF1Scores Man page
getF1Scores,GenRegRes-method Man page
getF1Scores,ThetaRegRes-method Man page
getFilterList Man page Source code
getFiltersOfInterest Source code
getGOEvidenceCodes Man page Source code
getGOFromFeatures Man page Source code
getGONamespace Source code
getLisacol Man page Source code
getMarkerClasses Man page Source code
getMarkerMatClasses Source code
getMarkerVecClasses Source code
getMarkers Man page Source code
getMartInstanceList Man page Source code
getMartTab Man page Source code
getMatMarkers Source code
getNN Source code
getNewClusters Source code
getNormDist Man page Source code
getOldcol Man page Source code
getParams Man page
getParams,ClustRegRes-method Man page
getParams,GenRegRes-method Man page
getParams,ThetaRegRes-method Man page
getPrediction Source code
getPredictions Man page Source code
getRegularisedParams Man page
getRegularisedParams,GenRegRes-method Man page
getRegularizedParams Man page
getRegularizedParams,GenRegRes-method Man page
getSeed Man page
getSeed,GenRegRes-method Man page
getStockcol Man page Source code
getStockpch Man page Source code
getUnknowncol Man page Source code
getUnknownpch Man page Source code
getVecMarkers Source code
getWarnings Man page
getWarnings,GenRegRes-method Man page
gmmOutlier Source code
goIdToTerm Man page Source code
goTermToId Man page Source code
highlightOnPlot Man page Source code
highlightOnPlot3D Man page Source code
isBinary Source code
isMrkMat Man page Source code
isMrkVec Man page Source code
knnClassification Man page Source code
knnOptimisation Man page Source code
knnOptimization Man page
knnPrediction Man page Source code
knnRegularisation Man page Source code
knntlClassification Man page Source code
knntlOptimisation Man page Source code
ksvmClassification Man page Source code
ksvmOptimisation Man page Source code
ksvmOptimization Man page
ksvmPrediction Man page Source code
ksvmRegularisation Man page Source code
lapply,ClustDistList-method Man page
lapply,MartInstanceList,ANY-method Man page
lapply,MartInstanceList-method Man page
learnOneClass Source code
length,ClustDistList-method Man page
levelPlot Man page
levelPlot,ClustRegRes-method Man page
levelPlot,GenRegRes-method Man page
levelPlot,QSep-method Man page
loopInTestStep Source code
lopims Man page Source code
lopims1 Man page Source code
lopims2 Man page Source code
lopims3 Man page Source code
lopims4 Man page Source code
lopims5 Man page Source code
mahalanobis Source code
makeCol3 Source code
makeF1matrix Source code
makeGoSet Man page Source code
makePartList Source code
make_ans Source code
markerMSnSet Man page Source code
markers Man page
matMarkerMSnSet Source code
matSampleMSnSet Source code
matUnknownMSnSet Source code
meanDist Source code
meanMarkerDist Source code
minClassScore Man page Source code
minMarkers Man page Source code
move2Ds Man page Source code
mrkConsProfiles Man page Source code
mrkEncoding Man page Source code
mrkHClust Man page Source code
mrkMatAndVec Man page Source code
mrkMatToVec Man page Source code
mrkVecToMat Man page Source code
nDatasets Man page Source code
names,ClustDistList-method Man page
names,QSep-method Man page
names<-,ClustDistList,ANY-method Man page
names<-,QSep,character-method Man page
nbClassification Man page Source code
nbOptimisation Man page Source code
nbOptimization Man page
nbPrediction Man page Source code
nbRegularisation Man page Source code
nndist Man page
nndist,MSnSet,missing-method Man page
nndist,matrix,matrix-method Man page
nndist,matrix,missing-method Man page
nndist-methods Man page
nndist_matrix Source code
nndist_msnset Source code
nndistx_matrix Source code
nnetClassification Man page Source code
nnetOptimisation Man page Source code
nnetOptimization Man page
nnetPrediction Man page Source code
nnetRegularisation Man page Source code
nologgin Source code
normDist Source code
onAttach Source code
opt Source code
optim.kmeans Source code
orderGoAnnotations Man page Source code
orgQuants Man page Source code
pRoloc Man page
pRoloc-defunct Man page
pRoloc-deprecated Man page
pRoloc-package Man page
pRolocmarkers Man page Source code
pdist Source code Source code
perTurboClassification Man page Source code
perTurboOptimisation Man page Source code
perTurboOptimization Man page
phat Source code
phenoDisco Man page Source code
pl Source code
plot,ClustDist,MSnSet-method Man page
plot,ClustDistList,missing-method Man page
plot,ClustRegRes,missing-method Man page
plot,GenRegRes,missing-method Man page
plot,QSep,missing-method Man page
plot,QSep-method Man page
plot,SpatProtVis,missing-method Man page
plot,ThetaRegRes,missing-method Man page
plot2D Man page Source code
plot2Dmethods Man page
plot2Ds Man page Source code
plot3D,MSnSet-method Man page
plotDist Man page Source code
plotQSep Source code
plotThetas Source code
plsdaClassification Man page Source code
plsdaOptimisation Man page Source code
plsdaOptimization Man page
plsdaPrediction Man page Source code
plsdaRegularisation Man page Source code
powerset Source code
predictionPerTurbo Source code
prettyGoTermId Man page Source code
print.plot2Ds Source code
qsep Man page Source code
refNormMeanOfNonNAPepSum Source code
refNormMedOfPepRatio Source code
remap Source code
rfClassification Man page Source code
rfOptimisation Man page Source code
rfOptimization Man page
rfPrediction Man page Source code
rfRegularisation Man page Source code
sampleMSnSet Man page Source code
sapply,ClustDistList-method Man page
sapply,MartInstanceList,ANY-method Man page
sapply,MartInstanceList-method Man page
sbig Source code
separateDataSet Source code
setAnnotationParams Man page Source code
setLisacol Man page Source code
setOldcol Man page Source code
setStockcol Man page Source code
setStockpch Man page Source code
setUnknowncol Man page Source code
setUnknownpch Man page Source code
show,AnnotationParams-method Man page
show,ClustDist-method Man page
show,ClustDistList-method Man page
show,ClustRegRes-method Man page
show,GenRegRes-method Man page
show,MartInstance-method Man page
show,QSep-method Man page
show,SpatProtVis-method Man page
show,ThetaRegRes-method Man page
showGOEvidenceCodes Man page Source code
showMrkMat Man page Source code
splitTh Source code
subsetAsDataFrame Source code
subsetMarkers Man page Source code
summariseMatList Source code
summary,QSep-method Man page
svmClassification Man page Source code
svmOptimisation Man page Source code
svmOptimization Man page
svmPrediction Man page Source code
svmRegularisation Man page Source code
testMSnSet Man page Source code
testMarkers Man page Source code
testPerTurbo Source code
testStep Source code
thetas Man page Source code
tracking Source code
trainingPerTurbo Source code
trainingStep Source code
trainingStepAutoSigma Source code
undocumented Man page
unknownMSnSet Man page Source code
updateobject Source code
validpRolocVisMethod Source code
vc.res Source code
vecMarkerMSnSet Source code
vecSampleMSnSet Source code
vecUnknownMSnSet Source code
viction Source code Source code
zerosInBinMSnSet Man page Source code

Files

CONDUCT.md
DESCRIPTION
NAMESPACE
NEWS
NEWS.md
R
R/AllGenerics.R
R/MLInterfaces.R
R/MSnSet.R
R/MartInterface.R
R/annotation.R
R/belief.R
R/chi2.R
R/clusterdist-framework.R
R/clusterdist-functions.R
R/clustering-framework.R
R/clustering-kmeans.R
R/distances.R
R/dynamics.R
R/environment.R
R/go.R
R/goannotations.R
R/goenv.R
R/hclust.R
R/lopims.R
R/machinelearning-framework-theta.R
R/machinelearning-framework.R
R/machinelearning-functions-PerTurbo.R
R/machinelearning-functions-knn.R
R/machinelearning-functions-knntl.R
R/machinelearning-functions-ksvm.R
R/machinelearning-functions-nb.R
R/machinelearning-functions-nnet.R
R/machinelearning-functions-plsda.R
R/machinelearning-functions-rf.R
R/machinelearning-functions-svm.R
R/machinelearning-utils.R
R/makeGoSet.R
R/markers.R
R/pRolocmarkers.R
R/perTurbo-algorithm.R
R/phenodisco.R
R/plotting.R
R/plotting2.R
R/plotting3.R
R/qsep.R
R/utils.R
R/vis.R
R/zzz.R
build
build/partial.rdb
build/vignette.rds
data
data/andy2011params.rda
data/dunkley2006params.rda
inst
inst/CITATION
inst/doc
inst/doc/HUPO_2011_poster.R
inst/doc/HUPO_2011_poster.Rnw
inst/doc/HUPO_2011_poster.pdf
inst/doc/HUPO_2014_poster.R
inst/doc/HUPO_2014_poster.Rnw
inst/doc/HUPO_2014_poster.pdf
inst/doc/pRoloc-goannotations.R
inst/doc/pRoloc-goannotations.Rmd
inst/doc/pRoloc-goannotations.html
inst/doc/pRoloc-ml.Rnw
inst/doc/pRoloc-ml.pdf
inst/doc/pRoloc-transfer-learning.R
inst/doc/pRoloc-transfer-learning.Rnw
inst/doc/pRoloc-transfer-learning.pdf
inst/doc/pRoloc-tutorial.Rnw
inst/doc/pRoloc-tutorial.pdf
inst/extdata
inst/extdata/dunkley2006pdunittest1.rda
inst/extdata/dunkley2006pdunittest2.rda
inst/extdata/dunkley2006pdunittest_20140408.rda
inst/extdata/marker_atha.rds
inst/extdata/marker_dmel.rds
inst/extdata/marker_ggal.rds
inst/extdata/marker_hsap.rds
inst/extdata/marker_mmus.rds
inst/extdata/marker_scer_sgd.rds
inst/extdata/marker_scer_uniprot.rds
inst/extdata/mil.rds
inst/extdata/params.rda
inst/extdata/params2.rda
inst/extdata/pdres.rda
inst/figs
inst/figs/plot2D-hexbin.png
inst/figs/plot2D-lda.png
inst/figs/plot2D-null-black.png
inst/figs/plot2D-null-cex.png
inst/figs/plot2D-null-pch-black.png
inst/figs/plot2D-null-pch.png
inst/figs/plot2D-null.png
inst/figs/plot2D-scree.png
inst/figs/plot2D.png
inst/scripts
inst/scripts/biomart.R
inst/scripts/dynamics.R
inst/scripts/test_pd.R
man
man/AnnotationParams-class.Rd
man/ClustDist-class.Rd
man/ClustDistList-class.Rd
man/GenRegRes-class.Rd
man/MLearn-methods.Rd
man/MartInstance-class.Rd
man/QSep-class.Rd
man/SpatProtVis-class.Rd
man/addGoAnnotations.Rd
man/addLegend.Rd
man/addMarkers.Rd
man/checkFeatureNamesOverlap.Rd
man/checkFvarOverlap.Rd
man/chi2-methods.Rd
man/classWeights.Rd
man/clustDist.Rd
man/defunct.Rd
man/empPvalues.Rd
man/exprsToRatios-methods.Rd
man/fDataToUnknown.Rd
man/filterBinMSnSet.Rd
man/filterMaxMarkers.Rd
man/filterMinMarkers.Rd
man/filterZeroCols.Rd
man/getGOFromFeatures.Rd
man/getMarkerClasses.Rd
man/getMarkers.Rd
man/getNormDist.Rd
man/getPredictions.Rd
man/getStockcol.Rd
man/goIdToTerm.Rd
man/highlightOnPlot.Rd
man/knnClassification.Rd
man/knnOptimisation.Rd
man/knntlClassification.Rd
man/knntlOptimisation.Rd
man/ksvmClassification.Rd
man/ksvmOptimisation.Rd
man/lopims.Rd
man/makeGoSet.Rd
man/markerMSnSet.Rd
man/markers.Rd
man/minMarkers.Rd
man/move2Ds.Rd
man/mrkConsProfiles.Rd
man/mrkHClust.Rd
man/nbClassification.Rd
man/nbOptimisation.Rd
man/nndist-methods.Rd
man/nnetClassification.Rd
man/nnetOptimisation.Rd
man/orderGoAnnotations.Rd
man/orgQuants.Rd
man/pRoloc-package.Rd
man/pRolocmarkers.Rd
man/perTurboClassification.Rd
man/perTurboOptimisation.Rd
man/phenoDisco.Rd
man/plot2D.Rd
man/plot2Ds.Rd
man/plotDist.Rd
man/plsdaClassification.Rd
man/plsdaOptimisation.Rd
man/rfClassification.Rd
man/rfOptimisation.Rd
man/sampleMSnSet.Rd
man/showGOEvidenceCodes.Rd
man/subsetMarkers.Rd
man/svmClassification.Rd
man/svmOptimisation.Rd
man/testMSnSet.Rd
man/testMarkers.Rd
man/thetas.Rd
man/undocumented.Rd
man/zerosInBinMSnSet.Rd
src
src/Makevars
src/Makevars.win
src/pRoloc.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test_SpatProtVis.R
tests/testthat/test_annotation.R
tests/testthat/test_classWeights.R
tests/testthat/test_clustDist.R
tests/testthat/test_data.R
tests/testthat/test_dist.R
tests/testthat/test_go.R
tests/testthat/test_goannotations.R
tests/testthat/test_markers.R
tests/testthat/test_ml.R
tests/testthat/test_plot2D.R
tests/testthat/test_qsep.R
tests/testthat/test_theta.R
tests/testthat/test_utils.R
vignettes
vignettes/Bugs.tex
vignettes/Figures
vignettes/Figures/F1boxplots.pdf
vignettes/Figures/ISL-2_16.pdf
vignettes/Figures/ISL-2_17.pdf
vignettes/Figures/Screenshot_PCA2.png
vignettes/Figures/ap1.png
vignettes/Figures/ap2.png
vignettes/Figures/bubble-andy.pdf
vignettes/Figures/knnboundaries.R
vignettes/Figures/knnboundaries.pdf
vignettes/Figures/msnset.ditaa
vignettes/Figures/msnset.png
vignettes/Figures/organelle_proteomics.ditaa
vignettes/Figures/organelle_proteomics.png
vignettes/Figures/phenodisco.pdf
vignettes/Figures/phenodisco.tex
vignettes/Figures/plot3D.png
vignettes/Figures/tsne.pdf
vignettes/Foreword.tex
vignettes/HUPO_2011_poster.Rnw
vignettes/HUPO_2014_poster.Rnw
vignettes/HUPO_2014_poster.tex
vignettes/Makefile
vignettes/figure
vignettes/pRoloc-goannotations.Rmd
vignettes/pRoloc-ml.Rnw
vignettes/pRoloc-transfer-learning.Rnw
vignettes/pRoloc-transfer-learning.tex
vignettes/pRoloc-tutorial.Rnw
vignettes/pRoloc.bib
vignettes/vigsrc
vignettes/vigsrc/HUPO_2011_poster.pdf
vignettes/vigsrc/HUPO_2014_poster.pdf
pRoloc documentation built on May 20, 2017, 10:26 p.m.