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.

AuthorLaurent Gatto and Lisa M. Breckels with contributions from Thomas Burger and Samuel Wieczorek
Date of publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk>
LicenseGPL-2
Version1.14.5
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

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

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