pRoloc: A unifying bioinformatics framework for spatial proteomics

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pRoloc")
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
Version1.14.6
https://github.com/lgatto/pRoloc

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: 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

addGoAnnotations Man page
addLegend Man page
addMarkers Man page
andy2011params Man page
AnnotationParams Man page
AnnotationParams-class Man page
as.data.frame.MartInstance Man page
as.data.frame.MartInstanceList Man page
checkFeatureNamesOverlap Man page
checkFvarOverlap Man page
chi2 Man page
chi2,matrix,matrix-method Man page
chi2,matrix,numeric-method Man page
chi2-methods Man page
chi2,numeric,matrix-method Man page
chi2,numeric,numeric-method Man page
class:AnnotationParams Man page
class:ClustDist Man page
class:ClustDistList Man page
class:GenRegRes Man page
class::QSep Man page
class:SpatProtVis Man page
class:ThetaRegRes Man page
classWeights Man page
clustDist Man page
ClustDist Man page
ClustDist-class Man page
ClustDistList Man page
[,ClustDistList,ANY,ANY,ANY-method Man page
[[,ClustDistList,ANY,ANY-method Man page
[[,ClustDistList,ANY,missing-method Man page
[,ClustDistList,ANY,missing,missing-method Man page
ClustDistList-class Man page
col1 Man page
col2 Man page
combineThetaRegRes Man page
data1 Man page
data2 Man page
dunkley2006params Man page
empPvalues Man page
exprsToRatios Man page
exprsToRatios-methods Man page
exprsToRatios,MSnSet-method Man page
f1Count Man page
f1Count,GenRegRes-method Man page
f1Count,ThetaRegRes-method Man page
favourPrimary Man page
fDataToUnknown Man page
filterAttrs Man page
filterBinMSnSet Man page
filterMaxMarkers Man page
filterMinMarkers Man page
filterZeroCols Man page
filterZeroRows Man page
flipGoTermId Man page
GenRegRes Man page
GenRegRes-class Man page
getAnnotationParams Man page
getF1Scores Man page
getF1Scores,GenRegRes-method Man page
getF1Scores,ThetaRegRes-method Man page
getFilterList Man page
getGOEvidenceCodes Man page
getGOFromFeatures Man page
getLisacol Man page
getMarkerClasses Man page
getMarkers Man page
getMartInstanceList Man page
getMartTab Man page
getNormDist Man page
getOldcol Man page
getParams Man page
getParams,ClustRegRes-method Man page
getParams,GenRegRes-method Man page
getParams,ThetaRegRes-method Man page
getPredictions Man page
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
getStockpch Man page
getUnknowncol Man page
getUnknownpch Man page
getWarnings Man page
getWarnings,GenRegRes-method Man page
goIdToTerm Man page
goTermToId Man page
highlightOnPlot Man page
highlightOnPlot3D Man page
isMrkMat Man page
isMrkVec Man page
knnClassification Man page
knnOptimisation Man page
knnOptimization Man page
knnPrediction Man page
knnRegularisation Man page
knntlClassification Man page
knntlOptimisation Man page
ksvmClassification Man page
ksvmOptimisation Man page
ksvmOptimization Man page
ksvmPrediction Man page
ksvmRegularisation Man page
lapply,ClustDistList-method Man page
lapply,MartInstanceList,ANY-method Man page
lapply,MartInstanceList-method Man page
length,ClustDistList-method Man page
levelPlot Man page
levelPlot,ClustRegRes-method Man page
levelPlot,GenRegRes-method Man page
levelPlot,QSep-method Man page
lopims Man page
lopims1 Man page
lopims2 Man page
lopims3 Man page
lopims4 Man page
lopims5 Man page
makeGoSet Man page
markerMSnSet Man page
markers Man page
MartInstance Man page
MartInstance-class Man page
MartInstanceList Man page
[,MartInstanceList,ANY,ANY,ANY-method Man page
[,MartInstanceList,ANY,ANY-method Man page
[[,MartInstanceList,ANY,ANY-method Man page
MartInstanceList-class Man page
[,MartInstanceList-method Man page
[[,MartInstanceList-method Man page
minClassScore Man page
minMarkers 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
move2Ds Man page
mrkEncoding Man page
mrkHClust Man page
mrkMatAndVec Man page
mrkMatToVec Man page
mrkVecToMat Man page
MSnSetMLean Man page
names<-,ClustDistList,ANY-method Man page
names,ClustDistList-method Man page
names<-,QSep,character-method Man page
names,QSep-method Man page
nbClassification Man page
nbOptimisation Man page
nbOptimization Man page
nbPrediction Man page
nbRegularisation Man page
nDatasets Man page
nndist Man page
nndist,matrix,matrix-method Man page
nndist,matrix,missing-method Man page
nndist-methods Man page
nndist,MSnSet,missing-method Man page
nnetClassification Man page
nnetOptimisation Man page
nnetOptimization Man page
nnetPrediction Man page
nnetRegularisation Man page
orderGoAnnotations Man page
orgQuants Man page
perTurboClassification Man page
perTurboOptimisation Man page
perTurboOptimization Man page
phenoDisco Man page
plot2D Man page
plot2Dmethods Man page
plot2Ds Man page
plot3D,MSnSet-method Man page
plot,ClustDistList,missing-method Man page
plot,ClustDist,MSnSet-method Man page
plot,ClustRegRes,missing-method Man page
plotDist Man page
plot,GenRegRes,missing-method Man page
plot,QSep-method Man page
plot,QSep,missing-method Man page
plot,SpatProtVis,missing-method Man page
plot,ThetaRegRes,missing-method Man page
plsdaClassification Man page
plsdaOptimisation Man page
plsdaOptimization Man page
plsdaPrediction Man page
plsdaRegularisation Man page
prettyGoTermId Man page
pRoloc Man page
pRoloc-defunct Man page
pRoloc-deprecated Man page
pRolocmarkers Man page
pRoloc-package Man page
qsep Man page
QSep Man page
QSep-class Man page
rfClassification Man page
rfOptimisation Man page
rfOptimization Man page
rfPrediction Man page
rfRegularisation Man page
sampleMSnSet Man page
sapply,ClustDistList-method Man page
sapply,MartInstanceList,ANY-method Man page
sapply,MartInstanceList-method Man page
setAnnotationParams Man page
setLisacol Man page
setOldcol Man page
setStockcol Man page
setStockpch Man page
setUnknowncol Man page
setUnknownpch Man page
show,AnnotationParams-method Man page
show,ClustDistList-method Man page
show,ClustDist-method Man page
show,ClustRegRes-method Man page
show,GenRegRes-method Man page
showGOEvidenceCodes Man page
show,MartInstance-method Man page
showMrkMat Man page
show,QSep-method Man page
show,SpatProtVis-method Man page
show,ThetaRegRes-method Man page
SpatProtVis Man page
SpatProtVis-class Man page
subsetMarkers Man page
summary,QSep-method Man page
svmClassification Man page
svmOptimisation Man page
svmOptimization Man page
svmPrediction Man page
svmRegularisation Man page
testMarkers Man page
testMSnSet Man page
ThetaRegRes Man page
ThetaRegRes-class Man page
thetas Man page
undocumented Man page
unknownMSnSet Man page
zerosInBinMSnSet Man page

Files

CONDUCT.md
DESCRIPTION
NAMESPACE
NEWS
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
README
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/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/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

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

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