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rcellminer (version 1.4.2)

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

Description

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

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Version

Version

1.4.2

License

LGPL-3

Maintainer

Augustin Luna

Last Published

February 15th, 2017

Functions in rcellminer (1.4.2)

MolData

Returns a MolData object.
elNetMolDataNCI60

NCI60 Molecular Data
crossCorsSpearman

Calculate Spearman's correlations with between rows of input matrices
getBinaryMutationData

Compute a binary gene mutation data matrix from SNP and other mutation event-level data.
getMinDrugActivityRepeatCor

Returns a table indicating, for each compound in a specified set, the least significant correlation and associated p-value between its replicate experiments.
getMedSenLineActivity

Returns a vector of median sensitive cell line activity (-logGI50) values for a set of compounds.
getSampleData,DrugData-method

Returns a data frame with sample information.
getRepeatAct

Returns an eSet object with drug repeat activity experiment data.
patternComparison

Compare an input pattern against a set of patterns.
getDrugActivityRepeatData

Returns a matrix containing repeat activity experiment data for a compound.
getSampleData,MolData-method

Returns a data frame with sample information.
isPublic

Check if an NSC ID is public
getDrugActivityData

Returns a matrix containing activity (-logGI50) data for a set of compounds.
restrictFeatureMat

Restricts a feature matrix to only include features associated with a specified gene set.
rowCors

Row-wise correlations
plotDrugSets

Produces a barplot of the average values for a set of NSCs with a error bar (one standard deviation)
plotStructures

Plot Structures
removeMolDataType

Remove molecular data type prefixes from features.
searchForNscs

Search for NSCs
getAct,DrugData-method

Returns an eSet object with drug activity data.
getSampleData

Returns a data frame with sample information.
runShinyCompareStructures

Run the Compare Structures Shiny App
getRepeatAct,DrugData-method

Returns an eSet object with drug repeat activity experiment data.
getFeatureAnnot,DrugData-method

Returns a list of data frames with feature information.
Drug_MOA_Key

A data frame with descriptive information for all compound mechanism of action (MOA) abbreviations used in CellMiner.
getDrugName

Get the drug names for a set of NSC identifiers.
plotStructuresFromNscs

Plot the structures for NSCs
selectCorrelatedRows

Select features that are correlated with a given feature (or one or more features from a set of features).
passRuleOf5

Checks if SMILES passes Lipinski's Rule of 5
getAllFeatureData

Returns a list of feature data matrices.
getESetList,MolData-method

Returns a list of eSet objects.
getMoaStr

Get MOA string
getNumDrugActivityRepeats

Returns a vector indicating the number of drug activity repeat experiments with available data for each member of a set of compounds.
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.
getFeatureAnnot

Returns a list of data frames with feature information.
MolData,list,MIAxE-method

Returns a MolData object.
passRuleOf5FromNsc

Checks if NSC passes Lipinski's Rule of 5
getFeatureDataFromMatList

Extract from a list of matrices the data associated with a set of features.
getAllFeatureData,MolData-method

Returns a list of feature data matrices.
getFingerprintList

Get a list of fingerprints for a set of compounds
loadNciColorSet

Returns a 60-element color set that matches the color set used on http://discover.nci.nih.gov/
getDrugActivityRange

Returns a vector of log activity range values for set of compounds.
getDrugMoaList

Get a list of applicable MOA strings for a drug.
loadCellminerPlotInfo

Returns data to plot CellMiner plots
plotDrugActivityRepeats

Plot NCI-60 drug activity profiles for repeat experiments.
rcdkplot

Plot molecules
runShinyCompoundBrowser

Run the Compound Browser
initialize,MolData-method

Returns a MolData object.
getSmiles

Get the SMILES strings for a set of NSC identifiers.
runShinyComparePlots

Run the Compare Plots Shiny App
[[<-,MolData-method

Assigns an eSet object to a specified position in a MolData object eSet list.
DrugData,eSet,eSet,MIAxE-method

Returns a DrugData object.
DrugData

Returns a DrugData object.
cmVersion

CellMiner Version
compareFingerprints

Compare Structure Fingerprints to NCI DTP Compounds
getAct

Returns an eSet object with drug activity data.
getFeatureAnnot,MolData-method

Returns a list of data frames with feature information.
getNumMissingLines

Returns a vector indicating the number of NCI-60 cell lines with missing activity data for set of compounds.
hasMoa

Check if NSC has Mechanism of Action (MOA) Annotation
getESetList

Returns a list of eSet objects.
[[,MolData-method

Returns an indexed eSet object from a MolData object eSet list.
getRsd

Computes the relative standard deviation values with respect to the columns of a matrix or data.frame.
DrugData-class

An S4 class to represent drug activity and related data recorded for a set of biological samples.
fingerprintList

A list of pre-computed fingerprints using getFingeprintList()
crossCors

Calculate cross-correlations with between rows of input matrices
getMoaToCompounds

Get a named list mapping MOA classes to associated compound sets.
plotCellMiner

Description: Produces CellMiner-like plots in R
runShinyApp

Run Shiny App
MolData-class

An S4 class to represent molecular data recorded for a set of biological samples.
drugDB

CellMiner Drug Response Values
getColumnQuantiles

Calculate quantile for the columns in a matrix
getMolDataMatrices

Returns a list of molecular data type matrices, with rownames in each matrix prefixed with a data type abbreviation.
getActivityRangeStats

Returns a table of activity range statistics for a set of compounds.
initialize,DrugData-method

Returns a DrugData object.
getMolDataType

Get the molecular data type prefixes for a set of features.