# rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines

## Documentation for package ‘rcellminer’ version 2.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.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.
parCorPatternComparison | Compare an input pattern against a set of patterns, excluding the predictive effect of a fixed pattern or set of patterns.
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
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)
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.