afmExtract function

Extract computed parameters from an afmexperiment

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

afmExtract(afmexperiment, params = list("YM", "AE", "ED"), 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.

Returns

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)