.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. |
cmVersion | CellMiner Version |
compareFingerprints | Compare Structure Fingerprints to NCI DTP Compounds |
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 | A list of pre-computed fingerprints using getFingeprintList() |
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. |
getFingerprintList | Get a list of fingerprints for a set of compounds |
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. |
passRuleOf5 | Checks if SMILES passes Lipinski's Rule of 5 |
passRuleOf5FromNsc | Checks if NSC passes Lipinski's Rule of 5 |
patternComparison | Compare an input pattern against a set of patterns. |
plotCellMiner | Description: Produces CellMiner-like plots in R |
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) |
plotStructures | Plot Structures |
plotStructuresFromNscs | Plot the structures for NSCs |
rcdkplot | Plot molecules |
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 |
runShinyApp | Run Shiny App |
runShinyComparePlots | Run the Compare Plots Shiny App |
runShinyCompareStructures | Run the Compare Structures Shiny App |
runShinyCompoundBrowser | Run the Compound Browser |
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. |