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PharmacoGx (version 1.1.6)
Analysis of Large-Scale Pharmacogenomic Data
Description
Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
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Version
Version
1.1.6
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Install
install.packages('PharmacoGx')
Monthly Downloads
51
Version
1.1.6
License
Artistic-2.0
Maintainer
Benjamin HaibeKains
Last Published
June 10th, 2016
Functions in PharmacoGx (1.1.6)
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cellNames<-
cellNames<- Generic
cellInfo
cellInfo Generic
cellNames
cellNames Generic
amcc
Calculate an Adaptive Matthews Correlation Coefficient
availablePSets
Return a table of PharmacoSets available for download
computeABC
Fits dose-response curves to data given by the user and returns the ABC of the fitted curves.
CMAPsmall
Connectivity Map Example PharmacoSet
cellInfo<-
cellInfo<- Generic
checkPSetStructure
A function to verify the structure of a PharmacoSet
CCLEsmall
Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet
dateCreated
dateCreated Generic
connectivityScore
Function computing connectivity scores between two signatures
computeSlope
Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input.
dim,PharmacoSet-method
Get the dimensions of a PharmacoSet
computeIC50
Fits dose-response curves to data given by the user and returns the IC50 of the fitted curve.
computeAmax
Fits dose-response curves to data given by the user and returns the Amax of the fitted curve. Amax: 100 - viability at maximum concentarion (in fitted curve)
cosinePerm
Computes the cosine similarity and significance using permutation test
computeAUC
Return AUC (Area Under the drug response curve) for an experiment of a pSet by taking its concentration and viability as input.
downloadPertSig
Download Drug Perturbation Signatures
downloadPSet
Download a PharmacoSet object
featureNames
featureNames Generic
drugPerturbationSig
Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis.
drugInfo
drugInfo Generic
drugNames<-
drugNames<- Generic
featureInfo<-
featureInfo<- Generic
featureInfo
featureInfo Generic
drugSensitivitySig
Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis.
drugNames
drugNames Generic
drugDoseResponseCurve
Plot drug response curve of a given drug and a given cell for a list of pSets (objects of the PharmacoSet class).
drugInfo<-
drugInfo<- Generic
pertNumber<-
pertNumber<- Generic
intersectList
Utility to find the intersection between a list of more than two vectors or lists
molecularProfiles
molecularProfiles Generic
GDSCsmall
Genomics of Drug Sensitivity in Cancer Example PharmacoSet
logLogisticRegression
Fits curves of the form E = E_inf + (1 - E_inf)/(1 + (c/EC50)^HS) to dose-response data points (c, E) given by the user and returns a vector containing estimates for HS, E_inf, and EC50.
intersectPSet
Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user.
gwc
Calculate the gwc score between two vectors, using either a weighted spearman or pearson correlation
HDAC_genes
HDAC Gene Signature
mcc
Compute a Mathews Correlation Coefficient
molecularProfiles<-
molecularProfiles<- Generic
PharmacoSet-class
A Class to Contain PharmacoGenomic datasets together with their curations
PharmacoSet
PharmacoSet constructor
phenoInfo
phenoInfo Generic
pSetName
pSetName Generic
sensitivityInfo<-
sensitivityInfo<- Generic
sensitivityMeasures
sensitivityMeasures Generic
pertNumber
pertNumber Generic
sensitivityInfo
sensitivityInfo Generic
sensitivityProfiles<-
sensitivityProfiles<- Generic
phenoInfo<-
phenoInfo<- Generic
[,PharmacoSet-method
`[`
subsetTo
A function to subset a PharmacoSet to data containing only specified drugs, cells and genes
summarizeMolecularProfiles
Takes molecular data from a PharmacoSet, and summarises them into one entry per drug
summarizeSensitivityProfiles
Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table
unionList
Utility to find the union between a list of more than two vectors or lists
showSigAnnot
Show the Annotations of a signature object
show,PharmacoSig-method
Show PharmacoGx Signatures
sensNumber
sensNumber Generic
show,PharmacoSet-method
Show a PharamcoSet
sensitivityProfiles
sensitivityProfiles Generic
sensNumber<-
sensNumber<- Generic