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


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Documentation for package ‘rcellminer’ version 1.0.1

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.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
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.
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
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)
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.
runShinyComparePlots Run the Compare Plots Shiny App
runShinyCompareStructures Run the Compare Structures Shiny App
runShinyCompoundBrowser Run the Compound Browser
selectCorrelatedRows Get other features above some threshold
selectCorrelatedRows2 Get other features above some threshold (merges results from selectCorrelatedRows, invoked for a given Y, and each element in a list of 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.