Class that contain data that can be plotted as a ROC curve.

Description

Container for data that represent a receiver-operator-characteristic curve, and that were generated from the data of the annotated positive and negative controls in a scored cellHTS object.

Creating Objects

new("ROC")

ROC(object, positives, negatives) with object being an cellHTS instance.

Slots

name:

a character of length 1 with the name of the experiment from which the ROC object derives.

assayType:

a character of length 1 with the type of screenning assay. Possible values are: "one-way assay" and "two-way assay".

TP:

a vector of integers of length 1000.

FP:

a vector of integers of length 1000.

posNames:

a character vector with the name of the positive controls.

negNames:

a character vector with the name of the negative controls.

Methods

show

Print a summary of the object.

plot

Plot the ROC curve corresponding to the object.

lines

Line plot of the ROC object.

Author(s)

Ligia Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

See Also

ROC

Examples

    showClass("ROC")
    showMethods(class="ROC")
  
    ## Not run: 
    data(KcViabSmall)
    x <- normalizePlates(KcViabSmall, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none")
    x <- scoreReplicates(x, sign="-", method="zscore")
    x <- summarizeReplicates(x, summary="mean")
    y <- ROC(x)
    plot(y)
    lines(y, col="green")
    show(y)
    
## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cellHTS2)
Loading required package: RColorBrewer
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cellHTS2/ROC-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ROC-class
> ### Title: Class that contain data that can be plotted as a ROC curve.
> ### Aliases: ROC-class show,ROC-method
> ### Keywords: classes
> 
> ### ** Examples
> 
>     showClass("ROC")
Class "ROC" [package "cellHTS2"]

Slots:
                                                                  
Name:       name assayType        TP        FP  posNames  negNames
Class: character character   integer   integer character character
>     showMethods(class="ROC")

Function "%&%":
 <not an S4 generic function>

Function "%in%":
 <not an S4 generic function>

Function ".DollarNames":
 <not an S4 generic function>

Function ".kv":
 <not an S4 generic function>

Function ".kv<-":
 <not an S4 generic function>

Function ".obo_subset":
 <not an S4 generic function>

Function ".obo_subset<-":
 <not an S4 generic function>

Function ".replaceSEW":
 <not an S4 generic function>

Function ".stanza":
 <not an S4 generic function>

Function ".stanza<-":
 <not an S4 generic function>

Function "AIC":
 <not an S4 generic function>

Function "BIC":
 <not an S4 generic function>

Function "BunchKaufman":
 <not an S4 generic function>

Function "Cholesky":
 <not an S4 generic function>

Function "DFS":
 <not an S4 generic function>

Function "DatPkgFactory":
 <not an S4 generic function>

Function "Definition":
 <not an S4 generic function>

Function "Dist":
 <not an S4 generic function>

Function "GO2AllProbes":
 <not an S4 generic function>

Function "GOAllFrame":
 <not an S4 generic function>

Function "GOFrame":
 <not an S4 generic function>

Function "GOID":
 <not an S4 generic function>

Function "GeneColorSet":
 <not an S4 generic function>

Function "GeneSet":
 <not an S4 generic function>

Function "GeneSetCollection":
 <not an S4 generic function>

Function "ID2EntrezID":
 <not an S4 generic function>

Function "ID2GO":
 <not an S4 generic function>

Function "ID2KEGG":
 <not an S4 generic function>

Function "KEGG2AllProbes":
 <not an S4 generic function>

Function "KEGG2heatmap":
 <not an S4 generic function>

Function "KEGGFrame":
 <not an S4 generic function>

Function "KEGGmnplot":
 <not an S4 generic function>

Function "Lfilter":
 <not an S4 generic function>

Function "Lkeyname":
 <not an S4 generic function>

Function "Lkeys":
 <not an S4 generic function>

Function "Lkeys<-":
 <not an S4 generic function>

Function "Llength":
 <not an S4 generic function>

Function "Ltablename":
 <not an S4 generic function>

Function "MAplot":
 <not an S4 generic function>

Function "Mbox":
 <not an S4 generic function>

Function "NSBS":
 <not an S4 generic function>

Function "Ontology":
 <not an S4 generic function>

Function "ROWNAMES":
 <not an S4 generic function>

Function "Rattribnames":
 <not an S4 generic function>

Function "Rattribnames<-":
 <not an S4 generic function>

Function "Rfilter":
 <not an S4 generic function>

Function "Rkeyname":
 <not an S4 generic function>

Function "Rkeys":
 <not an S4 generic function>

Function "Rkeys<-":
 <not an S4 generic function>

Function "Rle":
 <not an S4 generic function>

Function "Rlength":
 <not an S4 generic function>

Function "Rtablename":
 <not an S4 generic function>

Function "SQLKeywords":
 <not an S4 generic function>

Function "Schur":
 <not an S4 generic function>

Function "Secondary":
 <not an S4 generic function>

Function "Synonym":
 <not an S4 generic function>

Function "Term":
 <not an S4 generic function>

Function "Views":
 <not an S4 generic function>

Function "abstText":
 <not an S4 generic function>

Function "acc":
 <not an S4 generic function>

Function "active":
 <not an S4 generic function>

Function "active<-":
 <not an S4 generic function>

Function "addAttributes":
 <not an S4 generic function>

Function "addEdge":
 <not an S4 generic function>

Function "addNode":
 <not an S4 generic function>

Function "adj":
 <not an S4 generic function>

Function "adjacencyMatrix":
 <not an S4 generic function>

Function "aggregate":
 <not an S4 generic function>

Function "all.equal":
 <not an S4 generic function>

Function "allGeneIds":
 <not an S4 generic function>

Function "appendGates":
 <not an S4 generic function>

Function "applyFun":
 <not an S4 generic function>

Function "applyFun<-":
 <not an S4 generic function>

Function "applyGate":
 <not an S4 generic function>

Function "applyParams":
 <not an S4 generic function>

Function "applyParams<-":
 <not an S4 generic function>

Function "arpLim":
 <not an S4 generic function>

Function "articleTitle":
 <not an S4 generic function>

Function "as.array":
 <not an S4 generic function>

Function "as.env":
 <not an S4 generic function>

Function "as.factor":
 <not an S4 generic function>

Function "as.gateSet":
 <not an S4 generic function>

Function "as.matrix":
 <not an S4 generic function>

Function "as.table":
 <not an S4 generic function>

Function "attrDataItem":
 <not an S4 generic function>

Function "attrDataItem<-":
 <not an S4 generic function>

Function "attrDefaults":
 <not an S4 generic function>

Function "attrDefaults<-":
 <not an S4 generic function>

Function "authors":
 <not an S4 generic function>

Function "band":
 <not an S4 generic function>

Function "barplot":
 <not an S4 generic function>

Function "bcCategory":
 <not an S4 generic function>

Function "bcSubCategory":
 <not an S4 generic function>

Function "bfs":
 <not an S4 generic function>

Function "bg.correct":
 <not an S4 generic function>

Function "biplot":
 <not an S4 generic function>

Function "by":
 <not an S4 generic function>

Function "categoryName":
 <not an S4 generic function>

Function "categoryName<-":
 <not an S4 generic function>

Function "categorySubsetIds":
 <not an S4 generic function>

Function "categorySubsetIds<-":
 <not an S4 generic function>

Function "categoryToEntrezBuilder":
 <not an S4 generic function>

Function "cdfName":
 <not an S4 generic function>

Function "chartr":
 <not an S4 generic function>

Function "chgDefaults":
 <not an S4 generic function>

Function "childrenOf":
 <not an S4 generic function>

Function "chol":
 <not an S4 generic function>

Function "chol2inv":
 <not an S4 generic function>

Function "chrGraph":
 <not an S4 generic function>

Function "chromInfo":
 <not an S4 generic function>

Function "chromLengths":
 <not an S4 generic function>

Function "chromLocs":
 <not an S4 generic function>

Function "chromNames":
 <not an S4 generic function>

Function "classNameForDisplay":
 <not an S4 generic function>

Function "clearMemoryManagement":
 <not an S4 generic function>

Function "clearNode":
 <not an S4 generic function>

Function "close":
 <not an S4 generic function>

Function "clusteringCoefficient":
 <not an S4 generic function>

Function "collapse":
 <not an S4 generic function>

Function "collectionType":
 <not an S4 generic function>

Function "collectionType<-":
 <not an S4 generic function>

Function "colmetanames":
 <not an S4 generic function>

Function "coloring":
 <not an S4 generic function>

Function "coloring<-":
 <not an S4 generic function>

Function "columnMetadata":
 <not an S4 generic function>

Function "columnMetadata<-":
 <not an S4 generic function>

Function "columns":
 <not an S4 generic function>

Function "combineNodes":
 <not an S4 generic function>

Function "comment.SAX":
 <not an S4 generic function>

Function "commonColnames":
 <not an S4 generic function>

Function "complement":
 <not an S4 generic function>

Function "complete":
 <not an S4 generic function>

Function "complete.cases":
 <not an S4 generic function>

Function "computeExprSet":
 <not an S4 generic function>

Function "conditional":
 <not an S4 generic function>

Function "conditional<-":
 <not an S4 generic function>

Function "configureDatPkg":
 <not an S4 generic function>

Function "confint":
 <not an S4 generic function>

Function "connComp":
 <not an S4 generic function>

Function "contributor":
 <not an S4 generic function>

Function "contributor<-":
 <not an S4 generic function>

Function "coords":
 <not an S4 generic function>

Function "cor":
 <not an S4 generic function>

Function "count.links":
 <not an S4 generic function>

Function "count.mappedLkeys":
 <not an S4 generic function>

Function "count.mappedRkeys":
 <not an S4 generic function>

Function "count.mappedkeys":
 <not an S4 generic function>

Function "countLnodeHits":
 <not an S4 generic function>

Function "countMatches":
 <not an S4 generic function>

Function "countOverlaps":
 <not an S4 generic function>

Function "countRnodeHits":
 <not an S4 generic function>

Function "cov":
 <not an S4 generic function>

Function "cov2cor":
 <not an S4 generic function>

Function "coverage":
 <not an S4 generic function>

Function "creationDate":
 <not an S4 generic function>

Function "creationDate<-":
 <not an S4 generic function>

Function "crossprod":
 <not an S4 generic function>

Function "csolve":
 <not an S4 generic function>

Function "dataSource":
 <not an S4 generic function>

Function "dbBegin":
 <not an S4 generic function>

Function "dbBeginTransaction":
 <not an S4 generic function>

Function "dbBind":
 <not an S4 generic function>

Function "dbCallProc":
 <not an S4 generic function>

Function "dbClearResult":
 <not an S4 generic function>

Function "dbColumnInfo":
 <not an S4 generic function>

Function "dbCommit":
 <not an S4 generic function>

Function "dbConnect":
 <not an S4 generic function>

Function "dbDataType":
 <not an S4 generic function>

Function "dbDisconnect":
 <not an S4 generic function>

Function "dbDriver":
 <not an S4 generic function>

Function "dbExistsTable":
 <not an S4 generic function>

Function "dbFetch":
 <not an S4 generic function>

Function "dbGetException":
 <not an S4 generic function>

Function "dbGetInfo":
 <not an S4 generic function>

Function "dbGetPreparedQuery":
 <not an S4 generic function>

Function "dbGetQuery":
 <not an S4 generic function>

Function "dbGetRowCount":
 <not an S4 generic function>

Function "dbGetRowsAffected":
 <not an S4 generic function>

Function "dbGetStatement":
 <not an S4 generic function>

Function "dbHasCompleted":
 <not an S4 generic function>

Function "dbInfo":
 <not an S4 generic function>

Function "dbIsValid":
 <not an S4 generic function>

Function "dbListConnections":
 <not an S4 generic function>

Function "dbListFields":
 <not an S4 generic function>

Function "dbListResults":
 <not an S4 generic function>

Function "dbListTables":
 <not an S4 generic function>

Function "dbQuoteIdentifier":
 <not an S4 generic function>

Function "dbQuoteString":
 <not an S4 generic function>

Function "dbReadTable":
 <not an S4 generic function>

Function "dbRemoveTable":
 <not an S4 generic function>

Function "dbRollback":
 <not an S4 generic function>

Function "dbSendPreparedQuery":
 <not an S4 generic function>

Function "dbSendQuery":
 <not an S4 generic function>

Function "dbSetDataMappings":
 <not an S4 generic function>

Function "dbUnloadDriver":
 <not an S4 generic function>

Function "dbWriteTable":
 <not an S4 generic function>

Function "dbiDataType":
 <not an S4 generic function>

Function "dbmeta":
 <not an S4 generic function>

Function "dbschema":
 <not an S4 generic function>

Function "decode":
 <not an S4 generic function>

Function "degree":
 <not an S4 generic function>

Function "desc":
 <not an S4 generic function>

Function "desc<-":
 <not an S4 generic function>

Function "details":
 <not an S4 generic function>

Function "determinant":
 <not an S4 generic function>

Function "dfs":
 <not an S4 generic function>

Function "diag":
 <not an S4 generic function>

Function "diag<-":
 <not an S4 generic function>

Function "diff":
 <not an S4 generic function>

Function "direction":
 <not an S4 generic function>

Function "direction<-":
 <not an S4 generic function>

Function "disjoin":
 <not an S4 generic function>

Function "disjointBins":
 <not an S4 generic function>

Function "distance":
 <not an S4 generic function>

Function "distanceToNearest":
 <not an S4 generic function>

Function "docName":
 <not an S4 generic function>

Function "docName<-":
 <not an S4 generic function>

Function "drawGate":
 <not an S4 generic function>

Function "drop":
 <not an S4 generic function>

Function "droplevels":
 <not an S4 generic function>

Function "dumpGXL":
 <not an S4 generic function>

Function "eapply":
 <not an S4 generic function>

Function "edgeData":
 <not an S4 generic function>

Function "edgeData<-":
 <not an S4 generic function>

Function "edgeDataDefaults":
 <not an S4 generic function>

Function "edgeDataDefaults<-":
 <not an S4 generic function>

Function "edgeL":
 <not an S4 generic function>

Function "edgeMatrix":
 <not an S4 generic function>

Function "edgeNames":
 <not an S4 generic function>

Function "edgeSets":
 <not an S4 generic function>

Function "edgeWeights":
 <not an S4 generic function>

Function "edgemode":
 <not an S4 generic function>

Function "edgemode<-":
 <not an S4 generic function>

Function "edges":
 <not an S4 generic function>

Function "effectSize":
 <not an S4 generic function>

Function "elementLengths":
 <not an S4 generic function>

Function "elementMetadata":
 <not an S4 generic function>

Function "elementMetadata<-":
 <not an S4 generic function>

Function "elementNROWS":
 <not an S4 generic function>

Function "elementType":
 <not an S4 generic function>

Function "endElement.SAX":
 <not an S4 generic function>

Function "endoapply":
 <not an S4 generic function>

Function "entityDeclaration.SAX":
 <not an S4 generic function>

Function "erho":
 <not an S4 generic function>

Function "erhoLim":
 <not an S4 generic function>

Function "erhoLimD":
 <not an S4 generic function>

Function "evalSeparately":
 <not an S4 generic function>

Function "evidenceCode":
 <not an S4 generic function>

Function "exists":
 <not an S4 generic function>

Function "expand.grid":
 <not an S4 generic function>

Function "expectedCounts":
 <not an S4 generic function>

Function "expm":
 <not an S4 generic function>

Function "express.summary.stat":
 <not an S4 generic function>

Function "extractFromTo":
 <not an S4 generic function>

Function "extractList":
 <not an S4 generic function>

Function "extractROWS":
 <not an S4 generic function>

Function "facmul":
 <not an S4 generic function>

Function "fetch":
 <not an S4 generic function>

Function "filterRules":
 <not an S4 generic function>

Function "filterRules<-":
 <not an S4 generic function>

Function "findMatches":
 <not an S4 generic function>

Function "findOverlaps":
 <not an S4 generic function>

Function "findRange":
 <not an S4 generic function>

Function "findRun":
 <not an S4 generic function>

Function "findXIncludeStartNodes":
 <not an S4 generic function>

Function "first":
 <not an S4 generic function>

Function "first<-":
 <not an S4 generic function>

Function "flank":
 <not an S4 generic function>

Function "flatten":
 <not an S4 generic function>

Function "follow":
 <not an S4 generic function>

Function "forceSymmetric":
 <not an S4 generic function>

Function "formals<-":
 <not an S4 generic function>

Function "format":
 <not an S4 generic function>

Function "free":
 <not an S4 generic function>

Function "from":
 <not an S4 generic function>

Function "fromGXL":
 <not an S4 generic function>

Function "functions":
 <not an S4 generic function>

Function "gaps":
 <not an S4 generic function>

Function "gate":
 <not an S4 generic function>

Function "gate<-":
 <not an S4 generic function>

Function "geneColor":
 <not an S4 generic function>

Function "geneColor<-":
 <not an S4 generic function>

Function "geneCounts":
 <not an S4 generic function>

Function "geneIdType":
 <not an S4 generic function>

Function "geneIdType<-":
 <not an S4 generic function>

Function "geneIdUniverse":
 <not an S4 generic function>

Function "geneIds":
 <not an S4 generic function>

Function "geneIds<-":
 <not an S4 generic function>

Function "geneIdsByCategory":
 <not an S4 generic function>

Function "geneMappedCount":
 <not an S4 generic function>

Function "geneNames":
 <not an S4 generic function>

Function "geneSymbols":
 <not an S4 generic function>

Function "getBimapFilters":
 <not an S4 generic function>

Function "getCenter":
 <not an S4 generic function>

Function "getCorr":
 <not an S4 generic function>

Function "getCov":
 <not an S4 generic function>

Function "getData":
 <not an S4 generic function>

Function "getDet":
 <not an S4 generic function>

Function "getDistance":
 <not an S4 generic function>

Function "getEffectiveNamespaces":
 <not an S4 generic function>

Function "getEigenvalues":
 <not an S4 generic function>

Function "getEncoding":
 <not an S4 generic function>

Function "getEncodingREnum":
 <not an S4 generic function>

Function "getEvals":
 <not an S4 generic function>

Function "getFlag":
 <not an S4 generic function>

Function "getGOFrameData":
 <not an S4 generic function>

Function "getKEGGFrameData":
 <not an S4 generic function>

Function "getListElement":
 <not an S4 generic function>

Function "getLoadings":
 <not an S4 generic function>

Function "getMeth":
 <not an S4 generic function>

Function "getPrcomp":
 <not an S4 generic function>

Function "getQuan":
 <not an S4 generic function>

Function "getRaw":
 <not an S4 generic function>

Function "getScale":
 <not an S4 generic function>

Function "getScores":
 <not an S4 generic function>

Function "getSdev":
 <not an S4 generic function>

Function "getShape":
 <not an S4 generic function>

Function "getTableElementType":
 <not an S4 generic function>

Function "goSlim":
 <not an S4 generic function>

Function "graphData":
 <not an S4 generic function>

Function "graphData<-":
 <not an S4 generic function>

Function "graphIntersect":
 <not an S4 generic function>

Function "graphUnion":
 <not an S4 generic function>

Function "grouplengths":
 <not an S4 generic function>

Function "grouprank":
 <not an S4 generic function>

Function "gsub":
 <not an S4 generic function>

Function "hasMultiProbes":
 <not an S4 generic function>

Function "hasSingleProbes":
 <not an S4 generic function>

Function "head":
 <not an S4 generic function>

Function "high2low":
 <not an S4 generic function>

Function "hist":
 <not an S4 generic function>

Function "homoACC":
 <not an S4 generic function>

Function "homoHGID":
 <not an S4 generic function>

Function "homoLL":
 <not an S4 generic function>

Function "homoOrg":
 <not an S4 generic function>

Function "homoPS":
 <not an S4 generic function>

Function "homoType":
 <not an S4 generic function>

Function "homoURL":
 <not an S4 generic function>

Function "htmlReport":
 <not an S4 generic function>

Function "hyperGTest":
 <not an S4 generic function>

Function "hyperg":
 <not an S4 generic function>

Function "ids":
 <not an S4 generic function>

Function "ids<-":
 <not an S4 generic function>

Function "ifelse":
 <not an S4 generic function>

Function "inEdges":
 <not an S4 generic function>

Function "incidence":
 <not an S4 generic function>

Function "indexProbes":
 <not an S4 generic function>

Function "intensity":
 <not an S4 generic function>

Function "intensity<-":
 <not an S4 generic function>

Function "intersection":
 <not an S4 generic function>

Function "intersection2":
 <not an S4 generic function>

Function "isAdjacent":
 <not an S4 generic function>

Function "isClassic":
 <not an S4 generic function>

Function "isConnected":
 <not an S4 generic function>

Function "isConstant":
 <not an S4 generic function>

Function "isDBDatPkg":
 <not an S4 generic function>

Function "isDiagonal":
 <not an S4 generic function>

Function "isDirected":
 <not an S4 generic function>

Function "isDisjoint":
 <not an S4 generic function>

Function "isEmpty":
 <not an S4 generic function>

Function "isNA":
 <not an S4 generic function>

Function "isNormal":
 <not an S4 generic function>

Function "isSQLKeyword":
 <not an S4 generic function>

Function "isSingular":
 <not an S4 generic function>

Function "isSorted":
 <not an S4 generic function>

Function "isStrictlySorted":
 <not an S4 generic function>

Function "isSymmetric":
 <not an S4 generic function>

Function "isTriangular":
 <not an S4 generic function>

Function "iterM":
 <not an S4 generic function>

Function "iteratorFun":
 <not an S4 generic function>

Function "iteratorFun<-":
 <not an S4 generic function>

Function "join":
 <not an S4 generic function>

Function "journal":
 <not an S4 generic function>

Function "keyname":
 <not an S4 generic function>

Function "keys":
 <not an S4 generic function>

Function "keys<-":
 <not an S4 generic function>

Function "keytypes":
 <not an S4 generic function>

Function "leaves":
 <not an S4 generic function>

Function "level2nodes":
 <not an S4 generic function>

Function "levels":
 <not an S4 generic function>

Function "lgeneIds":
 <not an S4 generic function>

Function "linearMTest":
 <not an S4 generic function>
Function: lines (package graphics)
x="ROC"


Function "links":
 <not an S4 generic function>

Function "longDescription":
 <not an S4 generic function>

Function "longDescription<-":
 <not an S4 generic function>

Function "low2high":
 <not an S4 generic function>

Function "ls":
 <not an S4 generic function>

Function "lu":
 <not an S4 generic function>

Function "mainPage":
 <not an S4 generic function>

Function "make.db.names":
 <not an S4 generic function>

Function "makeValidParams":
 <not an S4 generic function>

Function "mapIdentifiers":
 <not an S4 generic function>

Function "mapIds":
 <not an S4 generic function>

Function "mapOrder":
 <not an S4 generic function>

Function "mappedLkeys":
 <not an S4 generic function>

Function "mappedRkeys":
 <not an S4 generic function>

Function "mappedkeys":
 <not an S4 generic function>

Function "mas5calls":
 <not an S4 generic function>

Function "maskedratio":
 <not an S4 generic function>

Function "maskedwidth":
 <not an S4 generic function>

Function "mcols":
 <not an S4 generic function>

Function "mcols<-":
 <not an S4 generic function>

Function "mean":
 <not an S4 generic function>

Function "median":
 <not an S4 generic function>

Function "members":
 <not an S4 generic function>

Function "mendoapply":
 <not an S4 generic function>

Function "merge":
 <not an S4 generic function>

Function "metadata":
 <not an S4 generic function>

Function "metadata<-":
 <not an S4 generic function>

Function "mgEdgeData":
 <not an S4 generic function>

Function "mgEdgeData<-":
 <not an S4 generic function>

Function "mgEdgeDataDefaults":
 <not an S4 generic function>

Function "mgEdgeDataDefaults<-":
 <not an S4 generic function>

Function "mid":
 <not an S4 generic function>

Function "mm":
 <not an S4 generic function>

Function "mm<-":
 <not an S4 generic function>

Function "mmindex":
 <not an S4 generic function>

Function "mstack":
 <not an S4 generic function>

Function "nChrom":
 <not an S4 generic function>

Function "nLnode":
 <not an S4 generic function>

Function "nRnode":
 <not an S4 generic function>

Function "na.exclude":
 <not an S4 generic function>

Function "na.omit":
 <not an S4 generic function>

Function "narrow":
 <not an S4 generic function>

Function "nchar":
 <not an S4 generic function>

Function "nearest":
 <not an S4 generic function>

Function "ngap":
 <not an S4 generic function>

Function "nhit":
 <not an S4 generic function>

Function "nir_list":
 <not an S4 generic function>

Function "nnode":
 <not an S4 generic function>

Function "nnzero":
 <not an S4 generic function>

Function "nobj":
 <not an S4 generic function>

Function "nobs":
 <not an S4 generic function>

Function "nodeData":
 <not an S4 generic function>

Function "nodeData<-":
 <not an S4 generic function>

Function "nodeDataDefaults":
 <not an S4 generic function>

Function "nodeDataDefaults<-":
 <not an S4 generic function>

Function "nodes":
 <not an S4 generic function>

Function "nodes<-":
 <not an S4 generic function>

Function "norm":
 <not an S4 generic function>

Function "normalize.methods":
 <not an S4 generic function>

Function "normalizeSingleBracketReplacementValue":
 <not an S4 generic function>

Function "nrun":
 <not an S4 generic function>

Function "numEdges":
 <not an S4 generic function>

Function "numNodes":
 <not an S4 generic function>

Function "oddsRatios":
 <not an S4 generic function>

Function "ontology":
 <not an S4 generic function>

Function "ontology<-":
 <not an S4 generic function>

Function "open":
 <not an S4 generic function>

Function "orderAsRanges":
 <not an S4 generic function>

Function "overlapsAny":
 <not an S4 generic function>

Function "pack":
 <not an S4 generic function>

Function "packageName":
 <not an S4 generic function>

Function "pageText":
 <not an S4 generic function>

Function "pageTitle":
 <not an S4 generic function>

Function "parallelSlotNames":
 <not an S4 generic function>

Function "parallelVectorNames":
 <not an S4 generic function>

Function "params":
 <not an S4 generic function>

Function "parentOf":
 <not an S4 generic function>

Function "pcompare":
 <not an S4 generic function>

Function "pcompareRecursively":
 <not an S4 generic function>

Function "pgap":
 <not an S4 generic function>

Function "phenotype":
 <not an S4 generic function>

Function "phenotype<-":
 <not an S4 generic function>

Function "phenotypeColor":
 <not an S4 generic function>

Function "phenotypeColor<-":
 <not an S4 generic function>

Function "pintersect":
 <not an S4 generic function>
Function: plot (package graphics)
x="ROC", y="missing"


Function "pm":
 <not an S4 generic function>

Function "pm<-":
 <not an S4 generic function>

Function "pmid":
 <not an S4 generic function>

Function "pmindex":
 <not an S4 generic function>

Function "poverlaps":
 <not an S4 generic function>

Function "precede":
 <not an S4 generic function>

Function "print":
 <not an S4 generic function>

Function "probeNames":
 <not an S4 generic function>

Function "probes":
 <not an S4 generic function>

Function "probesToChrom":
 <not an S4 generic function>

Function "probeset":
 <not an S4 generic function>

Function "process_self_hits":
 <not an S4 generic function>

Function "processingInstruction.SAX":
 <not an S4 generic function>

Function "profile":
 <not an S4 generic function>

Function "promoters":
 <not an S4 generic function>

Function "prompt":
 <not an S4 generic function>

Function "property":
 <not an S4 generic function>

Function "psetdiff":
 <not an S4 generic function>

Function "psi":
 <not an S4 generic function>

Function "pubDate":
 <not an S4 generic function>

Function "pubMedAbst":
 <not an S4 generic function>

Function "punion":
 <not an S4 generic function>

Function "pvalueCutoff":
 <not an S4 generic function>

Function "pvalueCutoff<-":
 <not an S4 generic function>

Function "pvalues":
 <not an S4 generic function>

Function "qr":
 <not an S4 generic function>

Function "qr.Q":
 <not an S4 generic function>

Function "qr.R":
 <not an S4 generic function>

Function "qr.coef":
 <not an S4 generic function>

Function "qr.fitted":
 <not an S4 generic function>

Function "qr.qty":
 <not an S4 generic function>

Function "qr.qy":
 <not an S4 generic function>

Function "qr.resid":
 <not an S4 generic function>

Function "quantile":
 <not an S4 generic function>

Function "rangedData":
 <not an S4 generic function>

Function "rangedData<-":
 <not an S4 generic function>

Function "ranges":
 <not an S4 generic function>

Function "ranges<-":
 <not an S4 generic function>

Function "rcond":
 <not an S4 generic function>

Function "rdapply":
 <not an S4 generic function>

Function "readHTMLList":
 <not an S4 generic function>

Function "readHTMLTable":
 <not an S4 generic function>

Function "readKeyValueDB":
 <not an S4 generic function>

Function "readSolrDoc":
 <not an S4 generic functio