This package contains methods and utilities for performing gene expression deconvolution, i.e. estimating cell type proportions and/or cell-specific gene expression signatures from global expression data in heterogeneous samples. Its main objectives are to provide:
See Algorithms for a list of all available deconvolution methods.
# install biocLite if not already there
if( !require(BiocInstaller) ){
# enable Bioconductor repositories
# -> add Bioc-software
setRepositories()
install.packages('BiocInstaller')
library(BiocInstaller)
}
# or alternatively do:
# source('http://www.bioconductor.org/biocLite.R')
# install (NB: this might ask you to update some of your packages)
biocLite('CellMix', siteRepos = 'http://web.cbio.uct.ac.za/~renaud/CRAN', type='both')
Abbas
addNames
applyBy
(applyBy.ExpressionSet, applyBy.matrix, colApplyBy, colMaxsBy, colMeansBy, colMediansBy, colMinsBy, colSumsBy, rowApplyBy, rowMaxsBy, rowMeansBy, rowMediansBy, rowMinsBy, rowSumsBy).atrack,MarkerList-method
barplot.MarkerList
basisfit
(coeffit)beeswarm.MarkerList
(hist.MarkerList, profplot.MarkerList, screeplot.MarkerList, stripchart.MarkerList)biocann_map
biocann_object
boxplotBy
(boxplotBy.default, boxplotBy.NMF)cbind.ExpressionSet
cellMarkers
(cellMarkersInfo)cellmix.options
(cellmix.getOption, cellmix.printOptions, cellmix.resetOptions)CellMix-package
(CellMix)checkConstraints
combine,MarkerList,factor-method
Compare,MarkerList,numeric-method
convertIDs
(convertIDs,ANY,ANY,ANY-method, convertIDs,ANY,ANY,NullIdentifier-method, convertIDs,ANY,list,missing-method, convertIDs,character,GeneIdentifierType,GeneIdentifierType-method, convertIDs,ExpressionSet,GeneIdentifierType,GeneIdentifierType-method, convertIDs,list,GeneIdentifierType,GeneIdentifierType-method, convertIDs,MarkerList,GeneIdentifierType,GeneIdentifierType-method, convertIDs,matrix,GeneIdentifierType,GeneIdentifierType-method, convertIDs-methods, mapIdentifiers,list,GeneIdentifierType,GeneIdentifierType-method)csplot
(csplot.character, csplot.NMFfit, csplot.NMFfitX).csSAM
csTopTable
(csTopTable.array, csTopTable.character, csTopTable.matrix, csTopTable.NMFfit, csTopTable.NMFfitX)DataSource
(isDataSource)dim,ExpressionMix-method
(dimnames<-,ExpressionMix,ANY-method, dimnames<-,ExpressionMix-method, dimnames,ExpressionMix-method, featureNames<-,ExpressionMix-method, sampleNames<-,ExpressionMix,ANY-method, sampleNames<-,ExpressionMix-method).DollarNames,ExpressionMix-method
dropvalues
(drop,MarkerList-method, hasDuplicated, mltype, nmark, nmark,ANY-method, nmark,list-method, nmark,MarkerList-method, nmark-methods, reverse, reverse,MarkerList-method, reverse-methods, rmDuplicated)DSAproportions
(.DSAproportions)DSection
enforceMarkers
(enforceMarkers,matrix,list-method, enforceMarkers,matrix,numeric-method, enforceMarkers-methods, enforceMarkers,NMF,ANY-method)eset
(eset,ExpressionMix-method, eset,GEDdata_entry-method, eset-methods)ExpressionMix
(ExpressionMix,character-method, ExpressionMix,ExpressionSet-method, ExpressionMix,matrix-method, ExpressionMix-methods, show,ExpressionMix-method)ExpressionMix-class
ExpressionMix-subset
([,ExpressionMix,ANY,ANY,ANY-method, [,ExpressionMix,ANY,ANY-method, [,ExpressionSet,MarkerList,ANY,ANY-method, [,ExpressionSet,MarkerList,ANY-method, [,MatrixData,MarkerList,ANY,ANY-method, [,MatrixData,MarkerList,ANY-method, [,NMF,MarkerList,ANY,ANY-method, [,NMF,MarkerList,ANY-method)extractMarkers
(extractMarkers,ANY-method, extractMarkers,ExpressionSet-method, extractMarkers-methods, markerScoreMethod, scoreMarkers)featureNames
(exprs, exprs,matrix-method, exprs-methods, featureNames<-, featureNames,MarkerList-method, featureNames,matrix-method, featureNames<--methods, featureNames-methods, sampleNames, sampleNames<-, sampleNames,matrix-method, sampleNames<--methods, sampleNames-methods)fetchData
flatten
(flatten,list-method, flatten,MarkerList-method, flatten-methods)ged
(ged,ANY,ANY,character-method, ged,ANY,ANY,function-method, ged,ANY,ANY,missing-method, ged,ExpressionSet,ANY,GEDStrategy-method, ged,MatrixData,ANY,GEDStrategy-method, ged-methods)gedAlgorithm
(gedAlgorithmInfo)gedAlgorithm.cs_lsfit
(cs-lsfit-ged)gedAlgorithm.csSAM
(csplot.csSAM, csSAM-ged, csTopTable.csSAM)gedAlgorithm.deconf
(deconf-ged)gedAlgorithm.DSA
(DSA-ged)gedAlgorithm.DSection
(csTopTable.DSection, DSection-ged)gedAlgorithm.lsfit
(lsfit-ged)gedAlgorithm.meanProfile
(meanProfile-ged)gedAlgorithm.qprog
(cs-qprog-ged, gedAlgorithm.cs_qprog, qprog-ged)gedAlgorithm.ssKL
(gedAlgorithm.ssFrobenius, ssFrobenius-ged, ssKL-ged)gedBlood
(asCBC, asCBC,character-method, asCBC,MarkerList-method, asCBC,matrix-method, asCBC-methods, asCBC,NMF-method, gCBC, refCBC)gedCheck
gedData
(gedDataInfo)GEDdata-access
(basis,GEDdata_entry-method, coef,GEDdata_entry-method, dims,GEDdata_entry-method, exprs,GEDdata_entry-method, nbasis,GEDdata_entry-method)GEDdownload
gedInput
(anyRequired, gedIO, gedOutput, isRequired, onlyRequired)gedProportions
GEDStrategy
(GEDStrategy,character-method, GEDStrategy,function-method, GEDStrategy,GEDalgorithm_entry-method, GEDStrategy,GEDStrategy-method, GEDStrategy-methods, GEDStrategy,missing-method)GEDStrategy-class
(show,GEDStrategy-method)geneValues
(annotation, annotation<-, annotation,GEDdata_entry-method, annotation<-,MarkerList,character-method, annotation,MarkerList-method, annotation<-,MarkerList,NULL-method, annotation<--methods, annotation-methods, connectivity, connectivity,MarkerList-method, connectivity-methods, details, details,MarkerList-method, details-methods, geneIds, geneIds<-, geneIds<-,MarkerList,list-method, geneIds,MarkerList-method, geneIds<--methods, geneIds-methods, geneIdType, geneIdType<-, geneIdType<-,MarkerList,character-method, geneIdType<-,MarkerList,GeneIdentifierType-method, geneIdType,MarkerList-method, geneIdType<-,MarkerList,NULL-method, geneIdType<--methods, geneIdType-methods, geneValues<-, geneValues,MarkerList-method, geneValues<--methods, geneValues-methods, hasValues, incidence, incidence,MarkerList-method, incidence-methods, marknames, marknames,list-method, marknames-methods, marknames,vector-method, nmf, nmf,MatrixData,MarkerList,ANY-method, nmf-methods, show,MarkerList-method)getGSE
gmarkers
(gMarkerList, rMarkerList, rmarkers)gpl2bioc
(bioc2gpl)GPL2bioc
Grigoryev-markers
GSE11058_pdata
GSE20300_pdata
GSE3649_fdata
GSE3649_pdata
HaemAtlas
hasAnnotation
(getAnnotation, setAnnotation)idFilter
(idFilterAffy, idFilterAll, idFilterAuto, idFilterFirstN, idFilterInjective, idFilterMAuto, idFilterOneToMany, idFilterOneToOne)idtype
(idtype,AnnDbBimap-method, idtype,ChipDb-method, idtype,ExpressionSet-method, idtype,GeneIdentifierType-method, idtype,list-method, idtype,MarkerList-method, idtype,matrix-method, idtype-methods, idtype,missing-method, idtype,NMF-method, idtype,NULL-method, idtype,ProbeAnnDbBimap-method, idtype,vector-method)initialize,ExpressionMix-method
intersect
(intersect,MatrixData,character-method, intersect,MatrixData,logical-method, intersect,MatrixData,MarkerList-method, intersect,MatrixData,MatrixData-method)IRIS
is.annpkg
(biocann_mapname, biocann_pkgname, biocann_pkgobject, is.anndb, revmap,character-method)is_logscale
(log_transform)is.probeid
(asGeneIdentifierType, is.idtype, is.probetype)kappa.MarkerList
log,ExpressionSet-method
(expb, expb,ExpressionSet-method, expb,matrix-method, expb-methods, exp,ExpressionSet-method, quantile.ExpressionSet, range,ExpressionSet-method).mAbbas
(Abbas-markers)mapIDs
MarkerList
(MarkerList,ANY-method, MarkerList,character-method, MarkerList,ExpressionSet-method, MarkerList,factor-method, MarkerList,integer-method, MarkerList,list-method, MarkerList,MarkerList-method, MarkerList,matrix-method, MarkerList-methods, MarkerList,missing-method, MarkerList,vector-method)[,MarkerList,ANY,ANY-method
([,MarkerList,ANY,ANY,ANY-method, [,MarkerList,list,ANY,ANY-method, [,MarkerList,list,ANY-method, [,MarkerList,missing,list,ANY-method, [,MarkerList,missing,list-method, subset,MarkerList-method)MarkerList-class
(attachMarkers, getMarkers, has.markers, isMarkerList, summary,MarkerList-method)markermap
(basismarkermap, markermap,MarkerList,ExpressionSet-method, markermap,MarkerList,matrix-method, markermap,MarkerList,NMFfitX-method, markermap,MarkerList,NMF-method, markermap,MatrixData,ANY-method, markermap-methods)markerScoreAbbas
markerScoreHSD
(selectMarkers.markerScore_HSD)markerScoreMaxcol
markerScoreScorem
(selectMarkers.markerScore_scorem)MarkerSetCollection
(MarkerSetCollection-methods)MarkerSetCollection-class
markersGrigoryev
match_first
matchIndex
(matchIndex,ANY,ANY-method, matchIndex,ANY,missing-method, matchIndex,list,character-method, matchIndex,list,ChipDb-method, matchIndex,list,ExpressionSet-method, matchIndex,list,matrix-method, matchIndex,list,NMF-method, matchIndex,list,ProbeAnnDbBimap-method, matchIndex-methods)match.nmf
(match.cell)mergeList
.mHaemAtlas
(HaemAtlas-markers).mIRIS
(IRIS-markers)mixData
(mixData<-, mixData,ExpressionMix-method, mixData<-,ExpressionMix,NMFstd-method, mixData<--methods, mixData-methods)mlsei
.mTDDB_HS
(TDDB_HS, TissueDistributionDB_HS-markers).mTDDB_RN
(TDDB_RN, TissueDistributionDB_RN-markers).mTIGER
(TIGER-markers)MySQLtoSQLite
npure
(lpure, mixedSamples, pureSamples, wpure)nuIDdecode
Palmer
propplot
regcheck
(checkS4)reorder,MarkerList-method
(sort.MarkerList)rmix
rproportions
rpure
sapply,MarkerList-method
selectGEDMethod
selectMarkers
(selectMarkers.MarkerList, selectMarkers.markerScore)setGEDMethod
(removeGEDMethod)setMarkerList
(removeMarkerList)showData
(showData,ExpressionMix-method, showData-methods)SLE
stack.MarkerList
(unstack.stackedMarkerList)subsetML
TIGER
TissueDistributionDB_HS
TissueDistributionDB_RN
userData
VeryGene
VeryGene-markers