| .DrugData | An S4 class to represent drug activity and related data recorded for a set of biological samples. |
| .MolData | An S4 class to represent molecular data recorded for a set of biological samples. |
| .onAttach | Display citation message |
| .onLoad | Make sure that rcellminerData is loaded |
| cmVersion | CellMiner Version |
| crossCors | Calculate cross-correlations with between rows of input matrices |
| crossCorsSpearman | Calculate Spearman's correlations with between rows of input matrices |
| 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-method | Returns a DrugData object. |
| drugDB | CellMiner Drug Response Values |
| Drug_MOA_Key | A data frame with descriptive information for all compound mechanism of action (MOA) abbreviations used in CellMiner. |
| elNetMolDataNCI60 | NCI60 Molecular Data |
| fingerprintList | Molecular Fingerprint List |
| getAct | Returns an eSet object with drug activity data. |
| getAct-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-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-method | Returns a list of eSet objects. |
| getFeatureAnnot | Returns a list of data frames with feature information. |
| getFeatureAnnot-method | Returns a list of data frames with feature information. |
| getFeatureAnnot-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-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-method | Returns a data frame with sample information. |
| getSampleData-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-method | Returns a DrugData object. |
| initialize-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-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. |
| [[-method | Returns an indexed eSet object from a MolData object eSet list. |
| [[<--method | Assigns an eSet object to a specified position in a MolData object eSet list. |