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Import raw .abf files as a dataframe

Source: R/Import-data.R
import_ABF_file.Rd

import_ABF_file() is a wrapper around abftools::abf2_load() and abftools::MeltAbf(). It converts the array from abf2_load() into a dataframe, and it also converts time to minutes.

Usage

import_ABF_file(file_name, recording_mode)

Arguments

file_name

Filepath to an .abf file (e.g. "Data/23711004.abf")

recording_mode

The mode used for the recording. If in recording_mode = "voltage_clamp" (e.g. clamping cell at -70 mV and measuring current amplitude) the primary channel (chan1) is set to "current" and the secondary channel (chan2) is "voltage". If recording_mode = "current_clamp", these values are reversed, where the primary channel is "voltage" and the secondary channel is "current".

Value

A dataframe with 5 or 6 columns, depending on the value of recording_mode.

  • time Time value from Clampfit which is in milliseconds x 10. For example, 5 seconds = 50000 in this column. Only appears if recording_mode = "current_clamp".

  • episode Character value (e.g. "epi1", "epi2") which corresponds directly to "sweep" in Clampfit.

  • current Current in pA.

  • voltage Voltage in mV.

  • time_sec Time in seconds. Note that this resets each sweep (for example, this may be 0 to 5 seconds for "epi1", then 0 to 5 seconds for "epi2"). For the cumulative elapsed time, see time_sec_total.

  • time_sec_total The total cumulative elapsed time in seconds. Useful for when you want to plot raw data vs. time for multiple sweeps.

Details

The file progresses from .abf to an array and then to a dataframe that can be easily manipulated in R. Be sure to assign a value to the dataframe so you can use it in later functions.

To export a flattened .abf file as a .csv file, you can use fwrite() from the data.table package.

Examples


import_ABF_file(import_ext_data("sample_abf.abf"), recording_mode = "voltage_clamp")

# To export this dataset as a csv use `fwrite()`
# from the `data.table` package and `here()` from the `here` package.

if (FALSE) { # \dontrun{
recording1 <- import_ABF_file(import_ext_data("sample_abf.abf"), recording_mode = "voltage_clamp")

} # }

#