.onAttach               Display citation message
.onLoad                 Make sure that rcellminerData is loaded
[[,MolData-method       Returns an indexed eSet object from a MolData
                        object eSet list.
[[<-,MolData-method     Assigns an eSet object to a specified position
                        in a MolData object eSet list.
cmVersion               CellMiner Version
crossCors               Calculate cross-correlations with between rows
                        of input matrices
crossCorsSpearman       Calculate Spearman's correlations with between
                        rows of input matrices
Drug_MOA_Key            A data frame with descriptive information for
                        all compound mechanism of action (MOA)
                        abbreviations used in CellMiner.
DrugData                Returns a DrugData object.
DrugData-class          An S4 class to represent drug activity and
                        related data recorded for a set of biological
                        samples.
DrugData,eSet,eSet,MIAxE-method
                        Returns a DrugData object.
drugDB                  CellMiner Drug Response Values
elNetMolDataNCI60       NCI60 Molecular Data
fingerprintList         Molecular Fingerprint List
getAct                  Returns an eSet object with drug activity data.
getAct,DrugData-method
                        Returns an eSet object with drug activity data.
getActivityRangeStats   Returns a table of activity range statistics
                        for a set of compounds.
getAllFeatureData       Returns a list of feature data matrices.
getAllFeatureData,MolData-method
                        Returns a list of feature data matrices.
getBinaryMutationData   Compute a binary gene mutation data matrix from
                        SNP and other mutation event-level data.
getColumnQuantiles      Calculate quantile for the columns in a matrix
getDrugActivityData     Returns a matrix containing activity (-logGI50)
                        data for a set of compounds.
getDrugActivityRange    Returns a vector of log activity range values
                        for set of compounds.
getDrugActivityRepeatData
                        Returns a matrix containing repeat activity
                        experiment data for a compound.
getDrugMoaList          Get a list of applicable MOA strings for a
                        drug.
getDrugName             Get the drug names for a set of NSC
                        identifiers.
getESetList             Returns a list of eSet objects.
getESetList,MolData-method
                        Returns a list of eSet objects.
getFeatureAnnot         Returns a list of data frames with feature
                        information.
getFeatureAnnot,DrugData-method
                        Returns a list of data frames with feature
                        information.
getFeatureAnnot,MolData-method
                        Returns a list of data frames with feature
                        information.
getFeatureDataFromMatList
                        Extract from a list of matrices the data
                        associated with a set of features.
getMedSenLineActivity   Returns a vector of median sensitive cell line
                        activity (-logGI50) values for a set of
                        compounds.
getMinDrugActivityRepeatCor
                        Returns a table indicating, for each compound
                        in a specified set, the least significant
                        correlation and associated p-value between its
                        replicate experiments.
getMoaStr               Get MOA string
getMoaToCompounds       Get a named list mapping MOA classes to
                        associated compound sets.
getMolDataMatrices      Returns a list of molecular data type matrices,
                        with rownames in each matrix prefixed with a
                        data type abbreviation.
getMolDataType          Get the molecular data type prefixes for a set
                        of features.
getNumDrugActivityRepeats
                        Returns a vector indicating the number of drug
                        activity repeat experiments with available data
                        for each member of a set of compounds.
getNumMissingLines      Returns a vector indicating the number of
                        NCI-60 cell lines with missing activity data
                        for set of compounds.
getRepeatAct            Returns an eSet object with drug repeat
                        activity experiment data.
getRepeatAct,DrugData-method
                        Returns an eSet object with drug repeat
                        activity experiment data.
getRsd                  Computes the relative standard deviation values
                        with respect to the columns of a matrix or
                        data.frame.
getSampleData           Returns a data frame with sample information.
getSampleData,DrugData-method
                        Returns a data frame with sample information.
getSampleData,MolData-method
                        Returns a data frame with sample information.
getSmiles               Get the SMILES strings for a set of NSC
                        identifiers.
hasMoa                  Check if NSC has Mechanism of Action (MOA)
                        Annotation
initialize,DrugData-method
                        Returns a DrugData object.
initialize,MolData-method
                        Returns a MolData object.
isPublic                Check if an NSC ID is public
loadCellminerPlotInfo   Returns data to plot CellMiner plots
loadNciColorSet         Returns a 60-element color set that matches the
                        color set used on http://discover.nci.nih.gov/
MolData                 Returns a MolData object.
MolData-class           An S4 class to represent molecular data
                        recorded for a set of biological samples.
MolData,list,MIAxE-method
                        Returns a MolData object.
parCorPatternComparison
                        Compare an input pattern against a set of
                        patterns, excluding the predictive effect of a
                        fixed pattern or set of patterns.
patternComparison       Compare an input pattern against a set of
                        patterns.
plotCellMiner           Description: Produces CellMiner-like plots in R
plotCellMiner2D         Make a simple 2d plot using two variables with
                        ggplot2
plotDrugActivityRepeats
                        Plot NCI-60 drug activity profiles for repeat
                        experiments.
plotDrugSets            Produces a barplot of the average values for a
                        set of NSCs with a error bar (one standard
                        deviation)
removeMolDataType       Remove molecular data type prefixes from
                        features.
restrictFeatureMat      Restricts a feature matrix to only include
                        features associated with a specified gene set.
rowCors                 Row-wise correlations
searchForNscs           Search for NSCs
selectCorrelatedRows    Select features that are correlated with a
                        given feature (or one or more features from a
                        set of features).
selectCorrelatedRowsFromMatrices
                        Select features that are correlated with a
                        given feature (or one or more features from a
                        set of features), merging results from multiple
                        candidate feature matrices.
