afmExtract: Extract computed parameters from an afmexperiment

In rbensua/afmToolkit: Functions for Atomic Force Microscope Force-Distance Curves Analysis

Description

Extracts some parameters from an afmexperiment for an easy further analysis.

Usage

afmExtract(afmexperiment, params = list("YM", "AE", "RE", "HY","AF","IF"), opt.param = NULL)

Arguments

afmexperiment	Data of afmexperiment class.
params	List of parameters to extract from the data.
opt.param	Optional parameter or factor in the params field of the afmdata list to add to the data extraction.

Value

A data frame with the name of the curve and the corresponding values of the parameters extacted.

Examples

## Not run: 
require(dplyr) # Not really necessary

# Load the data
data(batchExperiment)

# Process the afmexperiment
data <- afmContactPoint(batchExperiment, width = 50, mul1 = 1, mul2 = 10)
data <- afmDetachPoint(data, width = 50, mul1 = 1, mul2 = 10)
data <- afmBaselineCorrection(data)
data <- afmZeroPointSlope(data)
data <- afmIndentation(data)
data <- afmYoungModulus(data, thickness = 2e-7, params = list(alpha = 22))
data <- afmExpDecay(data, plt = FALSE)
data <- afmAdhesionEnergy(data, mul = 7)

# Extract the values of the parameters obtained in the analysis
afmExpParams <- afmExtract(data, opt.param = "type")

# Plotting the Young's Modulus
afmExpParams[[1]] %>% ggplot(aes(x = type, y = YM)) + geom_boxplot() 
ylab("Young's Modulus  (Pa)")

## End(Not run)

rbensua/afmToolkit documentation built on Dec. 1, 2020, 2:14 a.m.