The package can be installed from CRAN in the usual manner:
install.packages("readABF")
Alternatively, you can install the latest version from GitHub:
library(devtools)
install_github("Zabolekar/readABF")
library(readABF)
r <- readABF("some_data.abf")
plot(r)
For details, consult the package and functions documentation as accessed by ?
or help()
.
abf2, an R package by Matthew Caldwell: while abf2
only reads ABF2 files created by pClamp 10 and newer, we also support ABF files created by pClamp 9 and older, especially ABF version 1.83.
abfload, a MATLAB function by Harald Hentschke, Forrest Collman and Ulrich Egert: we try to read at least everything that abfload
is able to read. However, abfload
had some updates in 2017 which we haven't incorporated so far.
As you can notice, our tests/
directory is not published, neither on GitHub nor on CRAN. This has two reasons:
This package is tested (currently only under Linux) with the following combinations of file format versions and operation modes (each with multiple data sets):
| |variable-length event-driven|fixed-length event-driven|gap-free|episodic stimulation| |----|:--------------------------:|:-----------------------:|:------:|:------------------:| |1.65| | | |yes | |1.80| | |yes | | |1.83| | |yes |yes | |1.84|yes |yes |yes |yes | |2.00|no |yes |yes |yes |
Episodic stimulation mode is also sometimes called waveform fixed-length mode. High-speed oscilloscope mode is not tested due to lack of sample files.
We would very much appreciate to receive further data sets for testing purposes. A repository to upload data sets can be provided at request.
Support of Deutsche Forschungsgemeinschaft grant SFB 803 Z2 is gratefully acknowledged.
We would like to thank Harald Hentschke and his sources and the lab of Claudia Steinem for providing test data.
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