afmToolkit (version 1.0.0)

afmReadJPKMultiIndent: Read Nanowizard JPK ascii file containing a multi-indentation experiment

Description

Read an ascii JPK file containing several approach - pause segments and only one retract segment.

Usage

afmReadJPKMultiIndent(
  filename,
  path = "",
  FColStr = "Vertical Deflection",
  ZColStr = "Height (measured & smoothed)",
  tColStr = "Segment Time",
  silent = FALSE
)

Value

A afmdata structure list containing a field 'data' which is a data frame with variables Force, Z, Time (if aplicable) and Segment ("approach", "retract" and/or "pause") and a field 'params' which is a list with the fields 'curvename' and 'SpringConstant'.

Arguments

filename

String with the name of the jpk file.

path

Path to the folder where the file is.

FColStr

String with a pattern identifying the Force column.

ZColStr

String with a pattern identifying the Z column.

tColStr

String with a pattern identifying the Time column.

silent

Logical value. If TRUE suppresses the message indicating the name of the curve being processed (useful for batch-processing large number of curves). Defaults to FALSE

Examples

data <- afmReadJPKMultiIndent("force-save-JPK-multiIndent.txt.gz",path = path.package("afmToolkit"))
# Processing
data <- afmContactPoint(data, width = 100, mul1 = 1, mul2 = 10)
data <- afmDetachPoint(data, width = 100, mul1 = 1, mul2 = 10)
data <- afmBaselineCorrection(data)
data <- afmZeroPointSlope(data, fstar = 1)
data <- afmIndentation(data)
data <- afmRelax(data, model = "power", type = "CH", tmax = 5, plt = TRUE)