Function reference • sensorOverlord

Sensor Methods Functions defined on particular sensor objects
`error_df(<ligandSensor>)`	Finds the error df of this ligand sensor at given inaccuracies
`error_df(<pHSensor>)`	Finds the error df of this pH sensor at given inaccuracies
`error_df(<redoxSensor>)`	Finds the error df of this redox sensor at given inaccuracies
`getAbsError-R`(<redoxSensor>)	Get the error for a given sensor object at a given R
`getAbsError(<Sensor>)`	Get the error for a given sensor object
`getE(<redoxSensor>)`	Get the redox potential (E) for a redox sensor
`getE_deriv(<redoxSensor>)`	Get the derivative of the redox potential (dE/dR) for a redox sensor
`getErrorTable(<Sensor>)`	Get the error table for a given sensor object
`getFractionMax(<Sensor>)`	Get the fraction of sensors in the state corresponding to "Rmax"
`getProperty(<Sensor>)`	Get the fraction of sensors in the state corresponding to "Rmax" (wrapper)
`getProperty(<pHSensor>)`	Get the pH of a pH sensor (wrapper)
`getProperty(<redoxSensor>)`	Get the redox potential (E) for a redox sensor (wrapper)
`getR(<Sensor>)`	Method to get an array of R values from a sensor
`getpH(<pHSensor>)`	Get the pH of a pH sensor
`plotFractionMax(<Sensor>)`	Plot the fraction of sensors in the max state
`plotFractionMax(<pHSensor>)`	Plot the fraction of pH sensors in the max state
`plotFractionMax(<redoxSensor>)`	Plot the fraction of redox sensors in the max state
`plotProperty(<Sensor>)`	Plot the fraction max of a generic
`plotProperty(<pHSensor>)`	Plot the fraction of pH of a pHSensor
`plotProperty(<redoxSensor>)`	Plot the E of a redoxSensor
`rangePlot(<ligandSensor>)`	Make a plot of the suited ranges for this ligandSensor
`rangePlot(<pHSensor>)`	Make a plot of the suited ranges for this pHSensor
`rangePlot(<redoxSensor>)`	Make a plot of the suited ranges for this sensor
`ranges_df(<ligandSensor>)`	Finds the ranges df of this ligand sensor at given inaccuracies
`ranges_df(<pHSensor>)`	Finds the ranges df of this pH sensor at given inaccuracies
`ranges_df(<redoxSensor>)`	Finds the ranges df of this redox sensor at given inaccuracies
Spectra Methods Functions defined on particular spectra objects
`plotSpectra(<sensorSpectra>)`	Create a plot (ggplot object) for a sensorSpetra object
Biochemical values Utils functions for finding biochemical values
`E()`	What is the redox potential (mV), given R/Rmin/Rmax/delta/midpoint/temperature?
`pH()`	Finds pH, given R, Rmin, and Rmax
`pLigand()`	Finds pLigand, given R, Rmin, and Rmax
Errors Functions for finding errors in biochemical values
`Error_E()`	What is the error in redox potential at a given redox potential (mV), given some parameters of R and the error in R?
`Error_general()`	A general function for calculating the error in some parameter
`Error_pH()`	What is the error in pH at a given pH, given some parameters of R and the error in R?
`Error_pLigand()`	What is the error in pLigand at a given pLigand, given some parameters of R and the error in R?
`E()`	What is the redox potential (mV), given R/Rmin/Rmax/delta/midpoint/temperature?
`pH()`	Finds pH, given R, Rmin, and Rmax
`pLigand()`	Finds pLigand, given R, Rmin, and Rmax
`create_error_df_general()`	Creates a dataframe of errors at given inaccuracies
`create_error_df_pH()`	Creates a dataframe of errors in pH potential at given inaccuracies
`create_error_df_pH_multiple()`	Creates an error df at multiple inaccuracies, with multiple Rmin/Rmax/delta/pKa parameters
`create_error_df_pLigand()`	Creates a dataframe of errors in pLigand potential at given inaccuracies
`create_error_df_pLigand_multiple()`	Creates an error df at multiple inaccuracies, with multiple Rmin/Rmax/delta/pKd parameters
`create_error_df_redox()`	Creates a dataframe of errors in redox potential at given inaccuracies
`create_error_df_redox_multiple()`	Creates an error df at multiple inaccuracies, with multiple Rmin/Rmax/delta/e0 parameters
Ranges Functions for finding ranges of suitable biochemical values
`create_ranges_multiple()`	Takes in the input of create_error_df_redox_multiple and creates a simple ranges plot: e.g. minimum and maximum measureable value at different error thresholds for each sensor.
`plot_ranges_general()`	Takes in a ranges_df dataframe and makes a plot!
`plot_ranges_pH()`	Takes in a ranges_df dataframe and makes a plot (for pH).
`plot_ranges_pLigand()`	Takes in a ranges_df dataframe and makes a plot (for pLigand).
`plot_ranges_redox()`	Takes in a ranges_df dataframe and makes a plot (for redox).
`ranges_df(<ligandSensor>)`	Finds the ranges df of this ligand sensor at given inaccuracies
`ranges_df(<pHSensor>)`	Finds the ranges df of this pH sensor at given inaccuracies
`ranges_df(<redoxSensor>)`	Finds the ranges df of this redox sensor at given inaccuracies
`ranges_df()`	Find the ranges df of an object
Plots Plotting functions
`plotFractionMax(<Sensor>)`	Plot the fraction of sensors in the max state
`plotFractionMax(<pHSensor>)`	Plot the fraction of pH sensors in the max state
`plotFractionMax(<redoxSensor>)`	Plot the fraction of redox sensors in the max state
`plotProperty(<Sensor>)`	Plot the fraction max of a generic
`plotProperty(<pHSensor>)`	Plot the fraction of pH of a pHSensor
`plotProperty(<redoxSensor>)`	Plot the E of a redoxSensor
`plotSpectra(<sensorSpectra>)`	Create a plot (ggplot object) for a sensorSpetra object
`plot_ranges_general()`	Takes in a ranges_df dataframe and makes a plot!
`plot_ranges_pH()`	Takes in a ranges_df dataframe and makes a plot (for pH).
`plot_ranges_pLigand()`	Takes in a ranges_df dataframe and makes a plot (for pLigand).
`plot_ranges_redox()`	Takes in a ranges_df dataframe and makes a plot (for redox).
Errors Utils functions for finding errors in biochemical values
`Error_E()`	What is the error in redox potential at a given redox potential (mV), given some parameters of R and the error in R?
`Error_general()`	A general function for calculating the error in some parameter
`Error_pH()`	What is the error in pH at a given pH, given some parameters of R and the error in R?
`Error_pLigand()`	What is the error in pLigand at a given pLigand, given some parameters of R and the error in R?
All Functions A comprehensive list of all package functions
`E()`	What is the redox potential (mV), given R/Rmin/Rmax/delta/midpoint/temperature?
`Error_E()`	What is the error in redox potential at a given redox potential (mV), given some parameters of R and the error in R?
`Error_general()`	A general function for calculating the error in some parameter
`Error_pH()`	What is the error in pH at a given pH, given some parameters of R and the error in R?
`Error_pLigand()`	What is the error in pLigand at a given pLigand, given some parameters of R and the error in R?
`R_of_E()`	What was the recorded fluorescence ratio at a certain redox potential?
`R_of_pH()`	Finds R, given a pH
`R_of_pLigand()`	Finds R, given a pLigand
`Sensor-class`	An S4 class to represent a 2-state sensor
`adjustSpectra()`	Adjusts a spectra, assuming that the actual spectra is not limiting
`create_error_df_general()`	Creates a dataframe of errors at given inaccuracies
`create_error_df_pH()`	Creates a dataframe of errors in pH potential at given inaccuracies
`create_error_df_pH_multiple()`	Creates an error df at multiple inaccuracies, with multiple Rmin/Rmax/delta/pKa parameters
`create_error_df_pLigand()`	Creates a dataframe of errors in pLigand potential at given inaccuracies
`create_error_df_pLigand_multiple()`	Creates an error df at multiple inaccuracies, with multiple Rmin/Rmax/delta/pKd parameters
`create_error_df_redox()`	Creates a dataframe of errors in redox potential at given inaccuracies
`create_error_df_redox_multiple()`	Creates an error df at multiple inaccuracies, with multiple Rmin/Rmax/delta/e0 parameters
`create_ranges_multiple()`	Takes in the input of create_error_df_redox_multiple and creates a simple ranges plot: e.g. minimum and maximum measureable value at different error thresholds for each sensor.
`error_df(<ligandSensor>)`	Finds the error df of this ligand sensor at given inaccuracies
`error_df(<pHSensor>)`	Finds the error df of this pH sensor at given inaccuracies
`error_df(<redoxSensor>)`	Finds the error df of this redox sensor at given inaccuracies
`formatSpectraData()`	Formats sensor information into a dataframe suitable for input into database
`fraction_deprot()`	What is the fraction deprotenated of a certain pH, given the pKa? Note: this generalizes to any ligand-binding sensor type, given a pKa/pKd and a pLigand
`getAbsError-R`(<redoxSensor>)	Get the error for a given sensor object at a given R
`getAbsError(<Sensor>)`	Get the error for a given sensor object
`getDb()`	Returns the sensor database
`getE(<redoxSensor>)`	Get the redox potential (E) for a redox sensor
`getE_deriv(<redoxSensor>)`	Get the derivative of the redox potential (dE/dR) for a redox sensor
`getErrorTable(<Sensor>)`	Get the error table for a given sensor object
`getFractionMax(<Sensor>)`	Get the fraction of sensors in the state corresponding to "Rmax"
`getProperty(<Sensor>)`	Get the fraction of sensors in the state corresponding to "Rmax" (wrapper)
`getProperty(<pHSensor>)`	Get the pH of a pH sensor (wrapper)
`getProperty(<redoxSensor>)`	Get the redox potential (E) for a redox sensor (wrapper)
`getR(<Sensor>)`	Method to get an array of R values from a sensor
`getpH(<pHSensor>)`	Get the pH of a pH sensor
`launchApp()`	A wrapper function to run the included Shiny App
`ligandSensor-class`	An S4 class to represent a 2-state ligand sensor
`newSensorFromSpectra()`	A function to convert a sensorSpectra to a Sensor
`pH()`	Finds pH, given R, Rmin, and Rmax
`pHSensor-class`	An S4 class to represent a 2-state pH sensor
`pLigand()`	Finds pLigand, given R, Rmin, and Rmax
`plotFractionMax(<Sensor>)`	Plot the fraction of sensors in the max state
`plotFractionMax(<pHSensor>)`	Plot the fraction of pH sensors in the max state
`plotFractionMax(<redoxSensor>)`	Plot the fraction of redox sensors in the max state
`plotProperty(<Sensor>)`	Plot the fraction max of a generic
`plotProperty(<pHSensor>)`	Plot the fraction of pH of a pHSensor
`plotProperty(<redoxSensor>)`	Plot the E of a redoxSensor
`plotSpectra(<sensorSpectra>)`	Create a plot (ggplot object) for a sensorSpetra object
`plot_ranges_general()`	Takes in a ranges_df dataframe and makes a plot!
`plot_ranges_pH()`	Takes in a ranges_df dataframe and makes a plot (for pH).
`plot_ranges_pLigand()`	Takes in a ranges_df dataframe and makes a plot (for pLigand).
`plot_ranges_redox()`	Takes in a ranges_df dataframe and makes a plot (for redox).
`rangePlot(<ligandSensor>)`	Make a plot of the suited ranges for this ligandSensor
`rangePlot(<pHSensor>)`	Make a plot of the suited ranges for this pHSensor
`rangePlot(<redoxSensor>)`	Make a plot of the suited ranges for this sensor
`ranges_df(<ligandSensor>)`	Finds the ranges df of this ligand sensor at given inaccuracies
`ranges_df(<pHSensor>)`	Finds the ranges df of this pH sensor at given inaccuracies
`ranges_df(<redoxSensor>)`	Finds the ranges df of this redox sensor at given inaccuracies
`ranges_df()`	Find the ranges df of an object
`rescaleToRange()`	A function to rescale a certain (x,y) matrix pair into a new (x_new, y) pair.
`redoxSensor-class`	An S4 class to represent a 2-state redox sensor
`sensorSpectra-class`	An S4 class to represent the emission spectrum of a 2-state sensor
`spectraMatrixFromValues()`	A function to make a sensorSpectra from a set of 4 vectors

Reference

Sensor Methods

Spectra Methods

Biochemical values

Errors

Ranges

Plots

Errors

All Functions