Documentation

• Abbas
  Basis Matrix for Whole Blood Expression Deconvolution
• addNames
  Generating Names
• applyBy(applyBy.ExpressionSet, applyBy.matrix, colApplyBy, colMaxsBy, colMeansBy, colMediansBy, colMinsBy, colSumsBy, rowApplyBy, rowMaxsBy, rowMeansBy, rowMediansBy, rowMinsBy, rowSumsBy)
  Group Apply
• .atrack,MarkerList-method
  Heatmap Annotation Track for MarkerList Objects
• barplot.MarkerList
  Plotting MarkerList Objects
• basisfit(coeffit)
  Accessing Fit Data in Deconvolution Results
• beeswarm.MarkerList(hist.MarkerList, profplot.MarkerList, screeplot.MarkerList, stripchart.MarkerList)
  Plotting Markers
• biocann_map
  Retrieving ID Conversion Maps
• biocann_object
  Retrieving Bioconductor Annotation Maps
• boxplotBy(boxplotBy.default, boxplotBy.NMF)
  Split Boxplot by Group
• cbind.ExpressionSet
  Combining Expression Matrices
• cellMarkers(cellMarkersInfo)
  Loading Marker Lists from Registry
• cellmix.options(cellmix.getOption, cellmix.printOptions, cellmix.resetOptions)
  Package Specific Options for CellMix
• CellMix-package(CellMix)
  Gene Expression Deconvolution
• checkConstraints
  Checking Linear Constraints
• combine,MarkerList,factor-method
  Combine markers from multiple cell types of a MarkerList object, based on groups
• Compare,MarkerList,numeric-method
  Operations on MarkerList Objects
• 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)
  Converting Gene or Probeset IDs
• csplot(csplot.character, csplot.NMFfit, csplot.NMFfitX)
  Plots Cell-Specific FDR Estimates
• .csSAM
  Cell-specific Differential Expression with csSAM
• csTopTable(csTopTable.array, csTopTable.character, csTopTable.matrix, csTopTable.NMFfit, csTopTable.NMFfitX)
  Compute Cell-Specific Statistics
• DataSource(isDataSource)
  Gene Expression Data Sources
• dim,ExpressionMix-method(dimnames<-,ExpressionMix,ANY-method, dimnames<-,ExpressionMix-method, dimnames,ExpressionMix-method, featureNames<-,ExpressionMix-method, sampleNames<-,ExpressionMix,ANY-method, sampleNames<-,ExpressionMix-method)
  Dimensions in ExpressionMix Objects
• .DollarNames,ExpressionMix-method
  Auto-completion for
• 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)
  Utility Functions for MarkerList Objects
• DSAproportions(.DSAproportions)
  Digital Sorting Algorithm: Proportion Estimation Method
• DSection
  DSection Gene Expression Deconvolution Method
• enforceMarkers(enforceMarkers,matrix,list-method, enforceMarkers,matrix,numeric-method, enforceMarkers-methods, enforceMarkers,NMF,ANY-method)
  Enforcing Marker Block Patterns
• eset(eset,ExpressionMix-method, eset,GEDdata_entry-method, eset-methods)
  Extracting Expression Data
• ExpressionMix(ExpressionMix,character-method, ExpressionMix,ExpressionSet-method, ExpressionMix,matrix-method, ExpressionMix-methods, show,ExpressionMix-method)
  Factory Method for ExpressionMix Objects
• ExpressionMix-class
  Class for Gene Expression Deconvolution Benchmark Datasets
• 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)
  Subsetting ExpressionMix Objects
• extractMarkers(extractMarkers,ANY-method, extractMarkers,ExpressionSet-method, extractMarkers-methods, markerScoreMethod, scoreMarkers)
  Extract Markers from Pure Samples.
• 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)
  Extracting Feature Names
• fetchData
  Fetching Data from Data Sources
• flatten(flatten,list-method, flatten,MarkerList-method, flatten-methods)
  Flattening Marker Lists
• 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)
  Main Interface for Gene Expression Deconvolution Methods
• gedAlgorithm(gedAlgorithmInfo)
  Managing Gene Expression Deconvolution Algorithms
• gedAlgorithm.cs_lsfit(cs-lsfit-ged)
  Cell-Specific Expression by Standard Least-Squares
• gedAlgorithm.csSAM(csplot.csSAM, csSAM-ged, csTopTable.csSAM)
  Partial Gene Expression Deconvolution with csSAM
• gedAlgorithm.deconf(deconf-ged)
  Complete Gene Expression Deconvolution: Method deconf
• gedAlgorithm.DSA(DSA-ged)
  Complete Deconvolution using Digital Sorting Algorithm (DSA)
• gedAlgorithm.DSection(csTopTable.DSection, DSection-ged)
  Partial Gene Expression Deconvolution with DSection
• gedAlgorithm.lsfit(lsfit-ged)
  Partial Gene Expression Deconvolution by Standard Least-Squares
• gedAlgorithm.meanProfile(meanProfile-ged)
  Partial Gene Expression Deconvolution: Marker Mean Expression Profile
• gedAlgorithm.qprog(cs-qprog-ged, gedAlgorithm.cs_qprog, qprog-ged)
  Partial Gene Expression Deconvolution by Quadratic Programming
• gedAlgorithm.ssKL(gedAlgorithm.ssFrobenius, ssFrobenius-ged, ssKL-ged)
  Complete Gene Expression Deconvolution by Semi-Supervised NMF
• gedBlood(asCBC, asCBC,character-method, asCBC,MarkerList-method, asCBC,matrix-method, asCBC-methods, asCBC,NMF-method, gCBC, refCBC)
  Blood Sample Deconvolution
• gedCheck
  Checking a Deconvolution Method
• gedData(gedDataInfo)
  Loading Gene Expression Deconvolution Data
• GEDdata-access(basis,GEDdata_entry-method, coef,GEDdata_entry-method, dims,GEDdata_entry-method, exprs,GEDdata_entry-method, nbasis,GEDdata_entry-method)
  Accessing Data from CellMix Dataset
• GEDdownload
  Downloading Gene Expression Deconvolution Datasets
• gedInput(anyRequired, gedIO, gedOutput, isRequired, onlyRequired)
  Checking Input and Output Data for GED Algorithms
• gedProportions
  Estimating Cell Proportions from Known Signatures
• GEDStrategy(GEDStrategy,character-method, GEDStrategy,function-method, GEDStrategy,GEDalgorithm_entry-method, GEDStrategy,GEDStrategy-method, GEDStrategy-methods, GEDStrategy,missing-method)
  Factory Methods for GEDStrategy Objects
• GEDStrategy-class(show,GEDStrategy-method)
  Class for GED Algorithms
• 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)
  Accessing Data in Marker Lists
• getGSE
  Downloading GSE Datasets from GEO
• gmarkers(gMarkerList, rMarkerList, rmarkers)
  Generating Marker Lists
• gpl2bioc(bioc2gpl)
  Mapping Bioconductor Annotation packages to GEO GPL Identifiers
• GPL2bioc
  Map Between Bioconductor Annotation Packages and GEO GPL Identifiers
• Grigoryev-markers
  Grigoryev - Cytometry Antigen Markers
• GSE11058_pdata
  Cell Line Proportions for Dataset GSE11058
• GSE20300_pdata
  Complete Blood Count for Dataset GSE20300
• GSE3649_fdata
  Feature Annotation Data for Dataset GSE3649
• GSE3649_pdata
  Phenotypic Annotation Data for Dataset GSE3649
• HaemAtlas
  HaemAtlas Dataset - Immune Cells
• hasAnnotation(getAnnotation, setAnnotation)
  Extracting Annotation from Objects
• idFilter(idFilterAffy, idFilterAll, idFilterAuto, idFilterFirstN, idFilterInjective, idFilterMAuto, idFilterOneToMany, idFilterOneToOne)
  Gene Identifier Filtering Strategies
• 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)
  Identifying Gene or Probe ID Type
• initialize,ExpressionMix-method
  Initialize method for ExpressionMix object
• intersect(intersect,MatrixData,character-method, intersect,MatrixData,logical-method, intersect,MatrixData,MarkerList-method, intersect,MatrixData,MatrixData-method)
  Enhanced Subsetting for Matrix-like Data
• IRIS
  Immune Response In-Silico (IRIS) Data
• is.annpkg(biocann_mapname, biocann_pkgname, biocann_pkgobject, is.anndb, revmap,character-method)
  Annotation Tools
• is_logscale(log_transform)
  Detect Log-transformed Data
• is.probeid(asGeneIdentifierType, is.idtype, is.probetype)
  Utility function for Biological Identifiers
• kappa.MarkerList
  Condition Number of a Marker List
• log,ExpressionSet-method(expb, expb,ExpressionSet-method, expb,matrix-method, expb-methods, exp,ExpressionSet-method, quantile.ExpressionSet, range,ExpressionSet-method)
  Numeric Computations on ExpressionSet objects
• .mAbbas(Abbas-markers)
  Optimised Set of Marker Genes for Immune Cells
• mapIDs
  Mapping Gene Identifiers
• 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)
  Factory Method for Marker Lists
• [,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)
  Subsetting Marker Lists
• MarkerList-class(attachMarkers, getMarkers, has.markers, isMarkerList, summary,MarkerList-method)
  Class for Marker Gene Lists
• markermap(basismarkermap, markermap,MarkerList,ExpressionSet-method, markermap,MarkerList,matrix-method, markermap,MarkerList,NMFfitX-method, markermap,MarkerList,NMF-method, markermap,MatrixData,ANY-method, markermap-methods)
  Heatmaps Highlighting Markers
• markerScoreAbbas
  Marker Scoring Method: Abbas et al. (2009)
• markerScoreHSD(selectMarkers.markerScore_HSD)
  Marker Scoring Method: Tukey Honest Significant Difference
• markerScoreMaxcol
  Marker scoring method: Max Expression
• markerScoreScorem(selectMarkers.markerScore_scorem)
  Marker scoring method: SCOREM
• MarkerSetCollection(MarkerSetCollection-methods)
  Factory Methods for Marker Gene Set Collections
• MarkerSetCollection-class
  Classes for Marker Gene Set Collections
• markersGrigoryev
  Cytometry Antigen Expression from Grigoryev et al. (2010)
• match_first
  Returns the index of the first match in a reference table
• 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)
  Creating Mapping from Marker Lists
• match.nmf(match.cell)
  Assigning Estimated Signature to Real Cell-Types
• mergeList
  Merge two lists
• .mHaemAtlas(HaemAtlas-markers)
  HaemAtlas Marker List for Immune Cells - Watkins et al. (2009)
• .mIRIS(IRIS-markers)
  Marker Genes for Immune Cells (IRIS)
• mixData(mixData<-, mixData,ExpressionMix-method, mixData<-,ExpressionMix,NMFstd-method, mixData<--methods, mixData-methods)
  Extracting Mixture Data
• mlsei
  Multivariate Least Squares with Equalities and Inequalities
• .mTDDB_HS(TDDB_HS, TissueDistributionDB_HS-markers)
  Human Tissue Specific Genes from the TissueDistributionDB Database
• .mTDDB_RN(TDDB_RN, TissueDistributionDB_RN-markers)
  Rat Tissue Specific Genes from the TissueDistributionDB Database
• .mTIGER(TIGER-markers)
  TiGER - Human Tissue Specific Genes
• MySQLtoSQLite
  Load a MySQL Dump for Using with SQLite
• npure(lpure, mixedSamples, pureSamples, wpure)
  Acessing Pure or Mixed Sample Data
• nuIDdecode
  Convert nuID to Nucleotide Sequence
• Palmer
  Palmer Dataset
• propplot
  Cell Type Proportion Plot
• regcheck(checkS4)
  Validity Functions of Registry Fields
• reorder,MarkerList-method(sort.MarkerList)
  Reordering Marker Lists
• rmix
  Generating Random Global Mixed Gene Expression Data
• rproportions
  Generating Random Cell Type Proportions
• rpure
  Generating Random Pure Cell Type Sample
• sapply,MarkerList-method
  Aplying Functions Along MarkerList Objects
• selectGEDMethod
  Automatic Selection of Gene Expression Deconvolution Algorithms
• selectMarkers(selectMarkers.MarkerList, selectMarkers.markerScore)
  Select Markers Based on Scores
• setGEDMethod(removeGEDMethod)
  Register CellMix Deconvolution Methods
• setMarkerList(removeMarkerList)
  Register CellMix MarkerLists
• showData(showData,ExpressionMix-method, showData-methods)
  Show Data Available in an Object
• SLE
  Gene Expression from Systemic Lupus Erythematosus Patients
• stack.MarkerList(unstack.stackedMarkerList)
  Converting Marker Lists into data.frames
• subsetML
  Subsetting Data with MarkerList Objects
• TIGER
  TiGER Database
• TissueDistributionDB_HS
  Human Tissue Specific Genes from TissueDistributionDB
• TissueDistributionDB_RN
  Rat Tissue Specific Genes from TissueDistributionDB
• userData
  User Data Directory
• VeryGene
  VeryGene Dataset
• VeryGene-markers
  VeryGene - Marker List for Human Tissues