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

cmVersionCellMiner Version
compareFingerprintsCompare Structure Fingerprints to NCI DTP Compounds
crossCorsCalculate cross-correlations with between rows of input...
crossCorsSpearmanCalculate Spearman's correlations with between rows of input...
DrugDataReturns a DrugData object.
DrugData-classAn S4 class to represent drug activity and related data...
DrugData-eSet-eSet-MIAxE-methodReturns a DrugData object.
drugDBCellMiner Drug Response Values
Drug_MOA_KeyA data frame with descriptive information for all compound...
elNetMolDataNCI60NCI60 Molecular Data
fingerprintListA list of pre-computed fingerprints using getFingeprintList()
getActReturns an eSet object with drug activity data.
getAct-DrugData-methodReturns an eSet object with drug activity data.
getActivityRangeStatsReturns a table of activity range statistics for a set of...
getAllFeatureDataReturns a list of feature data matrices.
getAllFeatureData-MolData-methodReturns a list of feature data matrices.
getBinaryMutationDataCompute a binary gene mutation data matrix from SNP and other...
getColumnQuantilesCalculate quantile for the columns in a matrix
getDrugActivityDataReturns a matrix containing activity (-logGI50) data for a...
getDrugActivityRangeReturns a vector of log activity range values for set of...
getDrugActivityRepeatDataReturns a matrix containing repeat activity experiment data...
getDrugMoaListGet a list of applicable MOA strings for a drug.
getDrugNameGet the drug names for a set of NSC identifiers.
getESetListReturns a list of eSet objects.
getESetList-MolData-methodReturns a list of eSet objects.
getFeatureAnnotReturns a list of data frames with feature information.
getFeatureAnnot-DrugData-methodReturns a list of data frames with feature information.
getFeatureAnnot-MolData-methodReturns a list of data frames with feature information.
getFeatureDataFromMatListExtract from a list of matrices the data associated with a...
getFingerprintListGet a list of fingerprints for a set of compounds
getMedSenLineActivityReturns a vector of median sensitive cell line activity...
getMinDrugActivityRepeatCorReturns a table indicating, for each compound in a specified...
getMoaStrGet MOA string
getMoaToCompoundsGet a named list mapping MOA classes to associated compound...
getMolDataMatricesReturns a list of molecular data type matrices, with rownames...
getMolDataTypeGet the molecular data type prefixes for a set of features.
getNumDrugActivityRepeatsReturns a vector indicating the number of drug activity...
getNumMissingLinesReturns a vector indicating the number of NCI-60 cell lines...
getRepeatActReturns an eSet object with drug repeat activity experiment...
getRepeatAct-DrugData-methodReturns an eSet object with drug repeat activity experiment...
getRsdComputes the relative standard deviation values with respect...
getSampleDataReturns a data frame with sample information.
getSampleData-DrugData-methodReturns a data frame with sample information.
getSampleData-MolData-methodReturns a data frame with sample information.
getSmilesGet the SMILES strings for a set of NSC identifiers.
hasMoaCheck if NSC has Mechanism of Action (MOA) Annotation
initialize-DrugData-methodReturns a DrugData object.
initialize-MolData-methodReturns a MolData object.
isPublicCheck if an NSC ID is public
loadCellminerPlotInfoReturns data to plot CellMiner plots
loadNciColorSetReturns a 60-element color set that matches the color set...
MolDataReturns a MolData object.
MolData-classAn S4 class to represent molecular data recorded for a set of...
MolData-list-MIAxE-methodReturns a MolData object.
passRuleOf5Checks if SMILES passes Lipinski's Rule of 5
passRuleOf5FromNscChecks if NSC passes Lipinski's Rule of 5
patternComparisonCompare an input pattern against a set of patterns.
plotCellMinerDescription: Produces CellMiner-like plots in R
plotDrugActivityRepeatsPlot NCI-60 drug activity profiles for repeat experiments.
plotDrugSetsProduces a barplot of the average values for a set of NSCs...
plotStructuresPlot Structures
plotStructuresFromNscsPlot the structures for NSCs
rcdkplotPlot molecules
removeMolDataTypeRemove molecular data type prefixes from features.
restrictFeatureMatRestricts a feature matrix to only include features...
rowCorsRow-wise correlations
runShinyAppRun Shiny App
runShinyComparePlotsRun the Compare Plots Shiny App
runShinyCompareStructuresRun the Compare Structures Shiny App
runShinyCompoundBrowserRun the Compound Browser
searchForNscsSearch for NSCs
selectCorrelatedRowsSelect features that are correlated with a given feature (or...
selectCorrelatedRowsFromMatricesSelect features that are correlated with a given feature (or...
sub-sub-MolData-methodReturns an indexed eSet object from a MolData object eSet...
sub-subset-MolData-methodAssigns an eSet object to a specified position in a MolData...
rcellminer documentation built on May 31, 2017, 11:30 a.m.