A C D F G H I L M N P S T U misc
amcc | Adaptive Matthews Correlation Coefficient |
annotation | Accessing and modifying information in a 'PharmacoSet' |
annotation-method | Accessing and modifying information in a 'PharmacoSet' |
annotation<- | Accessing and modifying information in a 'PharmacoSet' |
annotation<--method | Accessing and modifying information in a 'PharmacoSet' |
availablePSets | Return a table of PharmacoSets available for download |
callingWaterfall | Drug sensitivity calling using waterfall plots |
CCLEsmall | Cancer Cell Line Encyclopedia (CCLE) Example PharmacoSet |
cellInfo | Accessing and modifying information in a 'PharmacoSet' |
cellInfo-method | Accessing and modifying information in a 'PharmacoSet' |
cellInfo<- | Accessing and modifying information in a 'PharmacoSet' |
cellInfo<--method | Accessing and modifying information in a 'PharmacoSet' |
cellName-method | Accessing and modifying information in a 'PharmacoSet' |
cellNames | Accessing and modifying information in a 'PharmacoSet' |
cellNames<- | Accessing and modifying information in a 'PharmacoSet' |
cellNames<--method | Accessing and modifying information in a 'PharmacoSet' |
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 | Cosine Permuations |
curation | Accessing and modifying information in a 'PharmacoSet' |
curation-method | Accessing and modifying information in a 'PharmacoSet' |
curation<- | Accessing and modifying information in a 'PharmacoSet' |
curation<--method | Accessing and modifying information in a 'PharmacoSet' |
datasetType | Accessing and modifying information in a 'PharmacoSet' |
datasetType-method | Accessing and modifying information in a 'PharmacoSet' |
datasetType<- | Accessing and modifying information in a 'PharmacoSet' |
datasetType<--method | Accessing and modifying information in a 'PharmacoSet' |
dateCreated | Accessing and modifying information in a 'PharmacoSet' |
dateCreated-method | Accessing and modifying information in a 'PharmacoSet' |
dateCreated<- | Accessing and modifying information in a 'PharmacoSet' |
dateCreated<--method | Accessing and modifying information in a 'PharmacoSet' |
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 | Accessing and modifying information in a 'PharmacoSet' |
drugInfo<- | Accessing and modifying information in a 'PharmacoSet' |
drugNames | Accessing and modifying information in a 'PharmacoSet' |
drugNames<- | Accessing and modifying information in a 'PharmacoSet' |
drugPerturbationSig | Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis. |
drugSensitivitySig-method | Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis. |
featureInfo | Accessing and modifying information in a 'PharmacoSet' |
featureInfo-method | Accessing and modifying information in a 'PharmacoSet' |
featureInfo<- | Accessing and modifying information in a 'PharmacoSet' |
featureInfo<--method | Accessing and modifying information in a 'PharmacoSet' |
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 | Accessing and modifying information in a 'PharmacoSet' |
fNames-method | Accessing and modifying information in a 'PharmacoSet' |
fNames<- | Accessing and modifying information in a 'PharmacoSet' |
fNames<--method | Accessing and modifying information in a 'PharmacoSet' |
GDSCsmall | Genomics of Drug Sensitivity in Cancer Example PharmacoSet |
geneDrugSensitivity | Calcualte The Gene Drug Sensitivity |
geneDrugSensitivityPBCorr | Calculate The Gene Drug Sensitivity |
geneDrugSensitivityPCorr | Calculate The Gene Drug Sensitivity |
gwc | GWC Score |
HDAC_genes | HDAC Gene Signature |
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 | Accessing and modifying information in a 'PharmacoSet' |
mDataNames-method | Accessing and modifying information in a 'PharmacoSet' |
mDataNames<- | Accessing and modifying information in a 'PharmacoSet' |
mDataNames<--method | Accessing and modifying information in a 'PharmacoSet' |
molecularProfiles | Accessing and modifying information in a 'PharmacoSet' |
molecularProfiles-method | Accessing and modifying information in a 'PharmacoSet' |
molecularProfiles<- | Accessing and modifying information in a 'PharmacoSet' |
molecularProfiles<--method | Accessing and modifying information in a 'PharmacoSet' |
molecularProfilesSlot | Accessing and modifying information in a 'PharmacoSet' |
molecularProfilesSlot-method | Accessing and modifying information in a 'PharmacoSet' |
molecularProfilesSlot<- | Accessing and modifying information in a 'PharmacoSet' |
molecularProfilesSlot<--method | Accessing and modifying information in a 'PharmacoSet' |
molecularProfilesSlot<-PharmacoSet-method | Accessing and modifying information in a 'PharmacoSet' |
moleculerProfilesSlot-method | Accessing and modifying information in a 'PharmacoSet' |
name | Accessing and modifying information in a 'PharmacoSet' |
name-method | Accessing and modifying information in a 'PharmacoSet' |
name<- | Accessing and modifying information in a 'PharmacoSet' |
name<--method | Accessing and modifying information in a 'PharmacoSet' |
patialCorQUICKSTOP | QUICKSTOP significance testing for partial correlation |
pertNumber | Accessing and modifying information in a 'PharmacoSet' |
pertNumber-method | Accessing and modifying information in a 'PharmacoSet' |
pertNumber<- | Accessing and modifying information in a 'PharmacoSet' |
pertNumber<--method | Accessing and modifying information in a 'PharmacoSet' |
PharmacoSet | PharmacoSet constructor |
PharmacoSet-accessors | Accessing and modifying information in a 'PharmacoSet' |
PharmacoSet-class | A Class to Contain PharmacoGenomic datasets together with their curations |
PharmacoSet-utils | Utility methods for a 'PharmacoSet' object. |
PharmacoSet2 | Make a CoreSet with the updated class structure |
PharmacoSig | Contructor for the PharmacoSig S4 class |
phenoInfo | Accessing and modifying information in a 'PharmacoSet' |
phenoInfo-method | Accessing and modifying information in a 'PharmacoSet' |
phenoInfo<- | Accessing and modifying information in a 'PharmacoSet' |
phenoInfo<--method | Accessing and modifying information in a 'PharmacoSet' |
plot.PharmacoSig | Plots a PharmacoSig object into a Volcano Plot |
sampleInfo | Accessing and modifying information in a 'PharmacoSet' |
sampleInfo-method | Accessing and modifying information in a 'PharmacoSet' |
sampleInfo<- | Accessing and modifying information in a 'PharmacoSet' |
sampleInfo<--method | Accessing and modifying information in a 'PharmacoSet' |
sampleName-method | Accessing and modifying information in a 'PharmacoSet' |
sampleNames | Accessing and modifying information in a 'PharmacoSet' |
sampleNames-method | Accessing and modifying information in a 'PharmacoSet' |
sampleNames<- | Accessing and modifying information in a 'PharmacoSet' |
sampleNames<--method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityInfo-method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityInfo<--method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityMeasures-method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityMeasures<--method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityProfiles-method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityProfiles<--method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityRaw-method | Accessing and modifying information in a 'PharmacoSet' |
sensitivityRaw<--method | Accessing and modifying information in a 'PharmacoSet' |
sensitivitySlot | Accessing and modifying information in a 'PharmacoSet' |
sensitivitySlot-method | Accessing and modifying information in a 'PharmacoSet' |
sensitivitySlot<- | Accessing and modifying information in a 'PharmacoSet' |
sensitivitySlot<--method | Accessing and modifying information in a 'PharmacoSet' |
sensitvityInfo<--method | Accessing and modifying information in a 'PharmacoSet' |
sensNumber | Accessing and modifying information in a 'PharmacoSet' |
sensNumber-method | Accessing and modifying information in a 'PharmacoSet' |
sensNumber<- | Accessing and modifying information in a 'PharmacoSet' |
sensNumber<--method | Accessing and modifying information in a 'PharmacoSet' |
show-method | Show a PharamcoSet |
show-method | Show PharmacoGx Signatures |
showSigAnnot-method | Show the Annotations of a signature object |
subsetByFeature | Utility methods for a 'PharmacoSet' object. |
subsetByFeature-method | Utility methods for a 'PharmacoSet' object. |
subsetBySample | Utility methods for a 'PharmacoSet' object. |
subsetBySample-method | Utility methods for a 'PharmacoSet' object. |
subsetByTreatment | Utility methods for a 'PharmacoSet' object. |
subsetByTreatment-method | Utility methods for a 'PharmacoSet' object. |
subsetTo-method | A function to subset a PharmacoSet to data containing only specified drugs, cells and genes |
summarizeSensitivityProfiles-method | Takes the sensitivity data from a PharmacoSet, and summarises them into a drug vs cell line table |
treatmentInfo | Accessing and modifying information in a 'PharmacoSet' |
treatmentInfo-method | Accessing and modifying information in a 'PharmacoSet' |
treatmentInfo<- | Accessing and modifying information in a 'PharmacoSet' |
treatmentInfo<--method | Accessing and modifying information in a 'PharmacoSet' |
treatmentNames | Accessing and modifying information in a 'PharmacoSet' |
treatmentNames-method | Accessing and modifying information in a 'PharmacoSet' |
treatmentNames<- | Accessing and modifying information in a 'PharmacoSet' |
treatmentNames<--method | Accessing and modifying information in a 'PharmacoSet' |
updateObject-method | Update the PharmacoSet class after changes in it struture or API |
.PharmacoSet | A Class to Contain PharmacoGenomic datasets together with their curations |
[-method | '[' |