afmToolkit (version 1.0.0)

afmExtract: Extract computed parameters from an afmexperiment

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,
  forces = NULL
)

Value

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

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.

forces

When one of the parameters to extract is the "Indentation Forces" ("IF"), this numeric vector provides the forces for which obtain the corresponding force. If forces is NULL (default), then the indentation at maximum force is computed.

Examples

if (FALSE) {
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)")
}