R: A class for data from cell-based high-throughput assays...
cellHTS-class
R Documentation
A class for data from cell-based high-throughput assays
performed in plate format.
Description
Container for data and experimental meta-data from cell-based
high-throughput assays performed in plate format.
Typical applications are RNA interference or small molecular compound screens.
The class extends the NChannelSet class.
Data are from experiments where the same set of reagents (probes) where used.
The class can represent data from multi-channel assays.
The data can be thought of as being organised in a two- or
three-dimensional array as follows:
The first dimension corresponds to reagents (e.g. siRNAs,
chemical compounds) that were used in the assays. For example, if
the screen used 100 plates of 384 wells (24 columns, 16 rows), then
the first dimension has size 38,400, and the cellHTS object
keeps track of plate ID, row, and column associated with each element.
For historic reasons, and because we are using infrastructure that
was developed for microarray experiments, the following terms are
used synonymously for the elements of the first dimension: reagents,
features, probes, genes.
The second dimension corresponds to assays, including
replicates and different experimental conditions (cell type,
treatment, genetic background). A potentially confusing terminology is that the data
structure that annotates the second dimension is called phenoData.
This is because we are using infrastructure
(the NChannelSet class) that
uses this unfortunate term for this purpose. The software provides
methodology for replicate summarization and scoring, however more
complicated experimental designs are not directly
supported. Multi-purpose tools like lmFit in the
limma package should be consulted.
The (optional) third dimension corresponds to different
channels (e.g. different luminescence reporters)
Objects from the Class
Objects can be created by calls of the form new("cellHTS",
assayData, phenoData, ...). See the examples below.
Slots
plateList:
a data.frame containing what
was read from input measurement data files plus a column
status of type character containing the string "OK" if the
data import appeared to have gone well, and the respective error
or warning message otherwise.
intensityFiles:
a list, where each component contains
a copy of the imported input data files. Its length corresponds to
the number of rows of plateList.
state:
a logical vector of length 4 representing the
processing status of the object. It must have the names
"configured", "normalized", "scored" and "annotated".
plateConf:
a data.frame containing what
was read from the configuration file for the experiment
(except the first two header rows). It contains at least three
columns named Plate, Well and Content.
Columns Plate and Well are allowed to contain
regular expressions.
screenLog:
a data.frame containing what
was read from the screen log file for the experiment, in
case it exists. Contains at least three columns, and column names
Plate, Well, and Flag. Additional columns are
Sample (when there are replicates or more than one sample
or condition) and Channel (when there are multiple
channels).
screenDesc:
a character containing what was read from
the description file of the experiment.
rowcol.effects:
a 3D array of size Features
(i.e. plate size x number of plates) x Samples x Channels
containing estimated row and column plate spatial offsets.
overall.effects:
a 3D array of size Features x
Samples x Channels containing estimated plate overall offsets.
assayData:
Object of class
AssayData, usually an
environment containing matrices of identical size. Each matrix
represents a single channel. Columns in each matrix correspond to
samples (or replicate), rows to features (probes). Once created,
cellHTS manages coordination of samples and channels.
plateData:
A list of data frames, with number of rows
of each frame equal to the number of plates used in the assay and
number of columns equal to the number of samples. Each data frame
in the list should contain factorial annotation information
relevant for the individual plates, like experimental batches or
varying types of micro-titre plates. Currently, this information
will be used for between-batch normalization and quality
assessment.
phenoData:
Object of class
AnnotatedDataFrame.
Please see the documentation of the phenoData slot of
NChannelSet for more
details.
It contains information about the screens, and it must have the
following columns in its data component: replicate
and assay, where replicate is expected to be a
vector of integers giving the replicate number, while assay
is expected to be a vector of characters giving the name of the
biological assay. Both of these vectors should have the same
length as the number of Samples.
Once created, cellHTS coordinates selection and subsetting
of channels in phenoData.
featureData:
Object of class
AnnotatedDataFrame,
containing information about the reagents: plate, well, column,
the well annotation (sample, control, etc.), etc. For a
cellHTS object, this slot must contain in its
data component at least three mandatory columns named
plate, well and controlStatus. Column
plate is expected to be a numeric vector giving the plate
number (e.g. 1, 2, ...), well should be a vector of
characters (alphanumeric characters) giving the well ID within the
plate (e.g. A01, B01, H12, etc.). Column controlStatus
should be a factor specifying the annotation for each well with
possible levels: empty, other, neg,
sample, and pos. Other levels besides pos and
neg may be employed for controls.
experimentData:
Object of class
MIAME containing descriptions
of the experiment.
annotation:
A "character" of length 1, which
can be used to specify the name of an annotation package that goes
with the reagents used for this experiment.
processingInfo:
A list containing information about
which normalization and summarization methods have been used.
.__classVersion__:
Object of class
Versions, containing
automatically created information about the class definition,
Biobase package version, and other information about the user
system at the time the instance was created. See
classVersion and
updateObject for examples of use.
Extends
Class NChannelSet, directly.
Methods
Methods with class-specific functionality:
name(object)
signature(object="cellHTS").
Obtains the name of the assay stored in the object. This
corresponds to the contents of column assay of the
phenoData slot of the cellHTS object.
name(object) <- value
signature(object =
"cellHTS", value = "character") assign the character of length
one (value) to the elements in column assay of the
slot phenoData of object.
pdim(object)
signature(object = "cellHTS").
Obtain the plate dimension for the data stored in object.
nbatch(object)
signature(object = "cellHTS").
Obtain the total number of batches for the data stored in object.
compare2cellHTS(x, y)
signature(x = "cellHTS",
y = "cellHTS"). Compares two cellHTS
objects, x and y, returning TRUE if they are
from the same experiment (i.e. if they derive from the same
initial cellHTS object), or FALSE otherwise.
Methods with functionality derived from class
NChannelSet:
channel, channelNames, channelNames<-, selectChannels,
object[features, samples], sampleNames
invoked automatically when the object is
displayed to the screen. It prints a summary of the object.
state
Access the state slot of a
cellHTS instance.
annotate
Annotate the cellHTS
object using the screen annotation file.
configure
Configure the cellHTS
object using the the screen description file, the
screen configuration file and the screen log file.
writeTab
Write the contents of assayData slot
of a cellHTS object to a tab-delimited file.
ROC
Construct an object of S4 class
ROC, which represents a
receiver-operator-characteristic curve, from the data of the
annotated positive and negative controls in a scored
cellHTS object.
meanSdPlot(x)
signature(x = "cellHTS") plots
row standard deviations across samples versus row means across
samples for data stored in slot assayData of a
cellHTS object. If there are multiple channels, row
standard deviations and row means are calculated across samples
for each channel separately. Only wells containing "sample" are
considered. See meanSdPlot for more details
about this function.
showClass("cellHTS")
showMethods(class="cellHTS")
## An empty cellHTS
obj <- new("cellHTS")
data("KcViabSmall")
KcViabSmall
state(KcViabSmall)
## Replicate 1 as a cellHTS object
y <- KcViabSmall[,1]
compare2cellHTS(KcViabSmall, y)
data("KcViab")
compare2cellHTS(KcViab, KcViabSmall)
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/cellHTS-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cellHTS-class
> ### Title: A class for data from cell-based high-throughput assays
> ### performed in plate format.
> ### Aliases: cellHTS-class cellHTS class.cellHTS show,cellHTS-method name
> ### name<- name,cellHTS-method name<-,cellHTS,character-method
> ### initialize,cellHTS-method nbatch nbatch,cellHTS-method
> ### compare2cellHTS compare2cellHTS,cellHTS,cellHTS-method meanSdPlot
> ### meanSdPlot,cellHTS-method coerce,chtsImage,data.frame-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("cellHTS")
Class "cellHTS" [package "cellHTS2"]
Slots:
Name: plateList intensityFiles state
Class: data.frameOrNULL list logical
Name: processingInfo plateConf screenLog
Class: list data.frameOrNULL data.frameOrNULL
Name: screenDesc rowcol.effects overall.effects
Class: character array array
Name: plateData assayData phenoData
Class: list AssayData AnnotatedDataFrame
Name: featureData experimentData annotation
Class: AnnotatedDataFrame MIAxE character
Name: protocolData .__classVersion__
Class: AnnotatedDataFrame Versions
Extends:
Class "NChannelSet", directly
Class "eSet", by class "NChannelSet", distance 2
Class "VersionedBiobase", by class "NChannelSet", distance 3
Class "Versioned", by class "NChannelSet", distance 4
> showMethods(class="cellHTS")
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: Data (package cellHTS2)
object="cellHTS"
Function: Data<- (package cellHTS2)
object="cellHTS", value="array"
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: ROC (package cellHTS2)
object="cellHTS"
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: annotate (package cellHTS2)
object="cellHTS"
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: batch (package cellHTS2)
object="cellHTS"
Function: batch<- (package cellHTS2)
object="cellHTS", value="data.frame"
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: compare2cellHTS (package cellHTS2)
x="cellHTS", y="cellHTS"
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: configure (package cellHTS2)
object="cellHTS"
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: geneAnno (package cellHTS2)
object="cellHTS"
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: initialize (package methods)
.Object="cellHTS"
Function "intensity":
<not an S4 generic function>
Function "intensity<-":
<not an S4 generic function>
Function: intensityFiles (package cellHTS2)
object="cellHTS"
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 "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: meanSdPlot (package vsn)
x="cellHTS"
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: name (package cellHTS2)
object="cellHTS"
Function: name<- (package cellHTS2)
object="cellHTS", value="character"
Function "narrow":
<not an S4 generic function>
Function: nbatch (package cellHTS2)
object="cellHTS"
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: pdim (package cellHTS2)
object="cellHTS"
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>
F