Man pages for cannin/rcellminer
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
| cmVersion | CellMiner Version |
| crossCors | Calculate cross-correlations with between rows of input... |
| crossCorsSpearman | Calculate Spearman's correlations with between rows of input... |
| dot-onAttach | Display citation message |
| dot-onLoad | Make sure that rcellminerData is loaded |
| DrugData | Returns a DrugData object. |
| DrugData-class | An S4 class to represent drug activity and related data... |
| DrugData-eSet-eSet-MIAxE-method | Returns a DrugData object. |
| drugDB | CellMiner Drug Response Values |
| Drug_MOA_Key | A data frame with descriptive information for all compound... |
| 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... |
| 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... |
| getColumnQuantiles | Calculate quantile for the columns in a matrix |
| getDrugActivityData | Returns a matrix containing activity (-logGI50) data for a... |
| getDrugActivityRange | Returns a vector of log activity range values for set of... |
| getDrugActivityRepeatData | Returns a matrix containing repeat activity experiment data... |
| 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... |
| getMedSenLineActivity | Returns a vector of median sensitive cell line activity... |
| getMinDrugActivityRepeatCor | Returns a table indicating, for each compound in a specified... |
| getMoaStr | Get MOA string |
| getMoaToCompounds | Get a named list mapping MOA classes to associated compound... |
| getMolDataMatrices | Returns a list of molecular data type matrices, with rownames... |
| getMolDataType | Get the molecular data type prefixes for a set of features. |
| getNumDrugActivityRepeats | Returns a vector indicating the number of drug activity... |
| getNumMissingLines | Returns a vector indicating the number of NCI-60 cell lines... |
| getRepeatAct | Returns an eSet object with drug repeat activity experiment... |
| getRepeatAct-DrugData-method | Returns an eSet object with drug repeat activity experiment... |
| getRsd | Computes the relative standard deviation values with respect... |
| 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... |
| MolData | Returns a MolData object. |
| MolData-class | An S4 class to represent molecular data recorded for a set of... |
| MolData-list-MIAxE-method | Returns a MolData object. |
| parCorPatternComparison | Compare an input pattern against a set of patterns, excluding... |
| 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... |
| removeMolDataType | Remove molecular data type prefixes from features. |
| restrictFeatureMat | Restricts a feature matrix to only include features... |
| rowCors | Row-wise correlations |
| searchForNscs | Search for NSCs |
| selectCorrelatedRows | Select features that are correlated with a given feature (or... |
| selectCorrelatedRowsFromMatrices | Select features that are correlated with a given feature (or... |
| sub-sub-MolData-method | Returns an indexed eSet object from a MolData object eSet... |
| sub-subset-MolData-method | Assigns an eSet object to a specified position in a MolData... |
