Package 'populationPDXdesign'

Title: Designing Population PDX Studies
Description: Run simulations to assess the impact of various designs features and the underlying biological behaviour on the outcome of a Patient Derived Xenograft (PDX) population study. This project can either be deployed to a server as a 'shiny' app or installed locally as a package and run the app using the command 'populationPDXdesignApp()'.
Authors: Maria Luisa Guerriero [aut, cre], Natasha Karp [aut]
Maintainer: Maria Luisa Guerriero <[email protected]>
License: GPL (>= 3)
Version: 1.0.3
Built: 2024-11-28 06:35:39 UTC
Source: CRAN

Help Index


Simulation of a single population PDX experiment

Description

This is an internal function. Please use cautiously if calling directly. Samples some animals and classify as responders or non-responders based on number of models studied (PDXn), number of mice measured per model (PDXr), the classification accuracy (C_Acc) and the underlying biological response rate (Biol_RR). Example usage: callsInSingleExperiment(PDXn=8, PDXr=3, C_Acc=0.95, Biol_RR=30)

Usage

callsInSingleExperiment(PDXn, PDXr, C_Acc, Biol_RR)

Arguments

PDXn

number of PDX models studied

PDXr

number of mice measured per PDX model

C_Acc

classification accuracy

Biol_RR

underlying biological response rate for this treatment

Value

dataframe with three columns:

- PDXModel is a string that indicates the model id

- PDXclassification is a numeric value that indicates the true biological classification of that PDX - 0 equal non-responder and 1 equal responder

- StudyResult is a numeric value that indicates the classification of the PDX model after sampling - 0 equal non-responder and 1 equal responder

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


Function to return the mode of a vector of values

Description

This is an internal function. Please use cautiously if calling directly. Returns the mode from numeric vector. Example usage: getMode(c(0,1,1))

Usage

getMode(v)

Arguments

v

vector of numeric values

Value

a numeric value

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


Function to calculate the number of false calls for a design for a go-no go threshold

Description

This is an internal function. Please use cautiously if calling directly. Returns the number of false calls from a simulation study exploring the impact of varying PDXn and PDXr for an underlying Biol_RR for a particularly go-no go threshold. A false call can only arise in the situation where the underlying Biol_RR is below the go-no go threshold. Example usage: noFalseCalls(ImpactVarying_PDXn_PDXr_BRR, GoNoGoThreshold=30)

Usage

noFalseCalls(dataset, GoNoGoThreshold)

Arguments

dataset

dataset obtained as output from the 'varying_PDXn_PDXr' function

GoNoGoThreshold

go-no go threshold

Value

vector with three elements:

- numeric value indicating the number of experiments simulated

- numeric value indicating the number of experiments which were above the go-no go threshold

- numeric value indicating the FPR

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


Function to calculate the number of missed calls for a design for a go-no go threshold

Description

This is an internal function. Please use cautiously if calling directly. Returns the number of missed calls from a simulation study exploring the impact of varying PDXn and PDXr for an underlying Biol_RR for a particularly go-no go threshold. A missed call can only arise in the situation where the underlying Biol_RR exceeds the go-no go threshold. Example usage: noMissedCalls(ImpactVarying_PDXn_PDXr_BRR, GoNoGoThreshold=30)

Usage

noMissedCalls(dataset, GoNoGoThreshold)

Arguments

dataset

dataset obtained as output from the 'varying_PDXn_PDXr' function

GoNoGoThreshold

go-no go threshold

Value

vector with three elements:

- numeric value indicating the number of experiments simulated

- numeric value indicating the number of experiments which were below the go-no go threshold

- numeric value indicating the percent of missed calls

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


Function to summarise the results for a single simulation representing one experiment

Description

This is an internal function. Please use cautiously if calling directly. From a simulation of a single experiment, the estimated response rate is determined and captured with the meta data (e.g. PDXn, PDXr) for that experiment. Example usage: outcomeInSingleExperiment(df=outcomeInSingleExperiment_1, PDXn=8, PDXr=3, C_Acc=0.95, Biol_RR=30)

Usage

outcomeInSingleExperiment(df, PDXn, PDXr, C_Acc, Biol_RR)

Arguments

df

data frame from callsInSingleExperiment

PDXn

PDXn

PDXr

PDXr

C_Acc

the classification accuracy (numeric value between 0 and 1)

Biol_RR

Biol_RR

Value

a vector with 8 values that captures the input design and the estimated response rate for that design from a single simulation

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


Function to run simulations to mimic population PDX studies for a defined scenario

Description

This is an internal function. Please use cautiously if calling directly. Simulations are used to mimic population PDX studies for specified values of PDXn, PDXr, Biol_RR and C_Acc. Example usage: outcomeMultipleExperiments(PDXn=8, PDXr=3, C_Acc=0.95, Biol_RR=30, iterations=500)

Usage

outcomeMultipleExperiments(PDXn, PDXr, C_Acc, Biol_RR, iterations)

Arguments

PDXn

PDXn

PDXr

PDXr

C_Acc

the classification accuracy (numeric value between 0 and 1)

Biol_RR

Biol_RR

iterations

no of experiments to simulated

Value

a dataframe where each row represents the results from a simulation mimicking an individual experiment for a particular design with meta data returned to describe the experimental design

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


A function to visualise the false postive rate as a function of PDXn and PDXr

Description

This is an internal function. Please use cautiously if calling directly. A visualisation of the false positive rate behaviour from the simulations

Usage

plotFalsepositive(data)

Arguments

data

data frame with four columns which indicate the PDXn, PDXr, Biol_RR and the FPR for a specified go-no go threshold

Value

a graphic visualisation

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


A function to visualise the sensitivity as a function of PDXn and PDXr

Description

This is an internal function. Please use cautiously if calling directly. A visualisation of the sensitivity from the simulations

Usage

plotSensitivity(data)

Arguments

data

data frame with four columns which indicate the PDXn, PDXr, Biol_RR and the MissedCalls for a specified go-no go threshold

Value

a graphic visualisation

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


Function populationPDXdesignApp

Description

Runs the 'shiny' app.

Usage

populationPDXdesignApp()

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]

Examples

if (interactive()) {
populationPDXdesignApp()
}

'shiny' app server function

Description

This is an internal function. Please use cautiously if calling directly

Usage

server(input, output, session)

Arguments

input

input

output

output

session

session

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


'shiny' app user interface function

Description

This is an internal function. Please use cautiously if calling directly.

Usage

ui()

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]


Function to run simulations to mimic population PDX studies for variety of experimental and biological scenarios

Description

This is an internal function. Please use cautiously if calling directly. Simulations are used to mimic population PDX studies by inputing a variety of experimental factors (PDXn and PDXr) and biological factors (Biol_RR and C_Acc). Example usage: varyingPDXnPDXrBiolRR(PDXn_range=c(8,10,12), PDXr_range=c(1,3,5), Biol_RR_range=c(30,40,50), C_Acc=0.95, iterations=500)

Usage

varyingPDXnPDXrBiolRR(PDXn_range, PDXr_range, Biol_RR_range, C_Acc, iterations)

Arguments

PDXn_range

a vector of PDXn values to study

PDXr_range

a vector of PDXr values to study

Biol_RR_range

a vector of values between 0 and 100 to indicate the Biol_RR to study

C_Acc

the classification accuracy (numeric value between 0 and 1)

iterations

iterations

Value

a dataframe where each row represents the results from a simulation mimicking an individual experiment for a particular design with meta data returned to describe the experimental design

Author(s)

Maria Luisa Guerriero, [email protected]

Natasha A. Karp, [email protected]