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

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Documentation for package ‘rcellminer’ version 2.22.0

• 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.
.onAttach	Display citation message
.onLoad	Make sure that rcellminerData is loaded
cmVersion	CellMiner Version
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	Molecular Fingerprint List
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.
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.
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)
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
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.