.PharmacoSet |
A Class to Contain PharmacoGenomic datasets together with their curations |
amcc |
Calculate an Adaptive Matthews Correlation Coefficient |
availablePSets |
Return a table of PharmacoSets available for download |
CCLEsmall |
Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet |
cellInfo |
cellInfo Generic |
cellInfo-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
cellInfo<- |
cellInfo<- Generic |
cellInfo<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
cellNames |
cellNames Generic |
cellNames-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
cellNames<- |
cellNames<- Generic |
cellNames<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
checkPSetStructure |
A function to verify the structure of a PharmacoSet |
CMAPsmall |
Connectivity Map Example PharmacoSet |
computeABC |
Fits dose-response curves to data given by the user and returns the ABC of the fitted curves. |
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) |
computeAUC |
Computes the AUC for a Drug Dose Viability Curve |
computeIC50 |
Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve |
computeICn |
Computes the ICn for any n in 0-100 for a Drug Dose Viability Curve |
computeSlope |
Return Slope (normalized slope of the drug response curve) for an experiment of a pSet by taking its concentration and viability as input. |
connectivityScore |
Function computing connectivity scores between two signatures |
cosinePerm |
Computes the cosine similarity and significance using permutation test |
dateCreated |
dateCreated Generic |
dateCreated-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
dim-method |
Get the dimensions of a PharmacoSet |
downloadPertSig |
Download Drug Perturbation Signatures |
downloadPSet |
Download a PharmacoSet object |
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 |
drugInfo-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
drugInfo<- |
drugInfo<- Generic |
drugInfo<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
drugNames |
drugNames Generic |
drugNames-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
drugNames<- |
drugNames<- Generic |
drugNames<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
drugPerturbationSig |
Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis. |
drugSensitivitySig |
Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis. |
featureInfo |
featureInfo Generic |
featureInfo-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
featureInfo<- |
featureInfo<- Generic |
featureInfo<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
filterNoisyCurves |
Viability measurements in dose-reponse curves must remain stable or decrease monotonically reflecting response to the drug being tested. filterNoisyCurves flags dose-response curves that strongly violate these assumptions. |
fNames |
fNames Generic |
fNames-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
GDSCsmall |
Genomics of Drug Sensitivity in Cancer Example PharmacoSet |
gwc |
Calculate the gwc score between two vectors, using either a weighted spearman or pearson correlation |
HDAC_genes |
HDAC Gene Signature |
intersectList |
Utility to find the intersection between a list of more than two vectors or lists |
intersectPSet |
Intersects objects of the PharmacoSet class, subsetting them to the common drugs and/or cell lines as selected by the user. |
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. |
mcc |
Compute a Mathews Correlation Coefficient |
mDataNames |
mDataNames |
molecularProfiles |
molecularProfiles Generic |
molecularProfiles-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
molecularProfiles<- |
molecularProfiles<- Generic |
molecularProfiles<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
pertNumber |
pertNumber Generic |
pertNumber-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
pertNumber<- |
pertNumber<- Generic |
pertNumber<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
PharmacoSet |
PharmacoSet constructor |
PharmacoSet-class |
A Class to Contain PharmacoGenomic datasets together with their curations |
phenoInfo |
phenoInfo Generic |
phenoInfo-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
phenoInfo<- |
phenoInfo<- Generic |
phenoInfo<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
pSetName |
pSetName Generic |
pSetName-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
sensitivityInfo |
sensitivityInfo Generic |
sensitivityInfo-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
sensitivityInfo<- |
sensitivityInfo<- Generic |
sensitivityInfo<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
sensitivityMeasures |
sensitivityMeasures Generic |
sensitivityMeasures-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
sensitivityProfiles |
sensitivityProfiles Generic |
sensitivityProfiles-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
sensitivityProfiles<- |
sensitivityProfiles<- Generic |
sensitivityProfiles<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
sensNumber |
sensNumber Generic |
sensNumber-method |
A Class to Contain PharmacoGenomic datasets together with their curations |
sensNumber<- |
sensNumber<- Generic |
sensNumber<--method |
A Class to Contain PharmacoGenomic datasets together with their curations |
show-method |
Show a PharamcoSet |
show-method |
Show PharmacoGx Signatures |
showSigAnnot |
Show the Annotations of a signature object |
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 |
symSetDiffList |
Utility to find the symmetric set difference of a list of two or more vectors or lists |
unionList |
Utility to find the union between a list of more than two vectors or lists |
[-method |
'[' |