afmToolkit
Functions for Atomic Force Microscope Force-Distance Curves Analysis

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afmExtract: Extract computed parameters from an afmexperiment

afmExtract: Extract computed parameters from an afmexperiment
In afmToolkit: Functions for Atomic Force Microscope Force-Distance Curves Analysis

Description Usage Arguments Value Examples

View source: R/afmExtract.R

Description

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

Usage

1
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.

Value

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

Examples

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## 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)

Example output

Loading required package: ggplot2
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

[1] "Processing curve:  force-save-2016.07.27-16.56.36.140.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.00.672.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.25.194.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.49.692.txt"
[1] "Processing curve:  force-save-2016.07.27-16.58.14.214.txt"
[1] "Processing curve:  force-save-2016.07.27-17.18.31.675.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.06.862.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.47.899.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.18.026.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.47.381.txt"
[1] "Processing curve:  force-save-2016.07.29-19.11.17.314.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341_001.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341.txt"
[1] "Processing curve:  force-save-2016.07.29-19.14.07.857.txt"
[1] "Processing curve:  force-save-2016.07.27-16.56.36.140.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.00.672.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.25.194.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.49.692.txt"
[1] "Processing curve:  force-save-2016.07.27-16.58.14.214.txt"
[1] "Processing curve:  force-save-2016.07.27-17.18.31.675.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.06.862.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.47.899.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.18.026.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.47.381.txt"
[1] "Processing curve:  force-save-2016.07.29-19.11.17.314.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341_001.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341.txt"
[1] "Processing curve:  force-save-2016.07.29-19.14.07.857.txt"
[1] "Processing curve:  force-save-2016.07.27-16.56.36.140.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.00.672.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.25.194.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.49.692.txt"
[1] "Processing curve:  force-save-2016.07.27-16.58.14.214.txt"
[1] "Processing curve:  force-save-2016.07.27-17.18.31.675.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.06.862.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.47.899.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.18.026.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.47.381.txt"
[1] "Processing curve:  force-save-2016.07.29-19.11.17.314.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341_001.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341.txt"
[1] "Processing curve:  force-save-2016.07.29-19.14.07.857.txt"
[1] "Processing curve:  force-save-2016.07.27-16.56.36.140.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.00.672.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.25.194.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.49.692.txt"
[1] "Processing curve:  force-save-2016.07.27-16.58.14.214.txt"
[1] "Processing curve:  force-save-2016.07.27-17.18.31.675.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.06.862.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.47.899.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.18.026.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.47.381.txt"
[1] "Processing curve:  force-save-2016.07.29-19.11.17.314.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341_001.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341.txt"
[1] "Processing curve:  force-save-2016.07.29-19.14.07.857.txt"
[1] "Processing curve:  force-save-2016.07.27-16.56.36.140.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.00.672.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.25.194.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.49.692.txt"
[1] "Processing curve:  force-save-2016.07.27-16.58.14.214.txt"
[1] "Processing curve:  force-save-2016.07.27-17.18.31.675.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.06.862.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.47.899.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.18.026.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.47.381.txt"
[1] "Processing curve:  force-save-2016.07.29-19.11.17.314.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341_001.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341.txt"
[1] "Processing curve:  force-save-2016.07.29-19.14.07.857.txt"
There were 15 warnings (use warnings() to see them)
[1] "Processing curve:  force-save-2016.07.27-16.56.36.140.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.00.672.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.25.194.txt"
[1] "Processing curve:  force-save-2016.07.27-16.57.49.692.txt"
[1] "Processing curve:  force-save-2016.07.27-16.58.14.214.txt"
[1] "Processing curve:  force-save-2016.07.27-17.18.31.675.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.06.862.txt"
[1] "Processing curve:  force-save-2016.07.29-18.47.47.899.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.18.026.txt"
[1] "Processing curve:  force-save-2016.07.29-18.50.47.381.txt"
[1] "Processing curve:  force-save-2016.07.29-19.11.17.314.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341_001.txt"
[1] "Processing curve:  force-save-2016.07.29-19.12.26.341.txt"
[1] "Processing curve:  force-save-2016.07.29-19.14.07.857.txt"
$y
[1] "Young's Modulus  (Pa)"

attr(,"class")
[1] "labels"

afmToolkit documentation built on May 1, 2019, 9:20 p.m.

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