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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

Install

install.packages('PharmacoGx')

Monthly Downloads

21

Version

1.1.6

License

Artistic-2.0

Maintainer

Benjamin HaibeKains

Last Published

June 10th, 2016

Functions in PharmacoGx (1.1.6)

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