Installation

The package can be installed as follows:

library(devtools)
install_github("Zabolekar/readABF")

It will be also submitted to CRAN very soon.

Usage

library(readABF)
r <- readABF("some_data.abf")
plot(r)

Difference to other packages

• 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 everything abfload was able to read as of Aug 1, 2012. However, abfload had some improvements in 2017, and we haven't incorporated them yet.

Tests

As you can notice, the tests/ directory is not published. This has two reasons:

• our test data is hundreds of megabytes large.
• we do not have the permission to share most of our test data.

Currently, code is tested under Linux only. This package is tested 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

• "yes" means: it's tested and it works.
• "no" means: it isn't implemented yet but we've tested that it gives an appropriate error message.
• empty cell means: it might work but it isn't tested.

Episodic stimulation mode is also sometimes called waveform fixed-length mode. High-speed oscilloscope mode wasn't tested due to lack of sample files.

We would very much appreciate to receive further data sets for testing purposes. A reporsitory to upload data sets can be provided at request.

Acknowledgements

• 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 us test data.