Skip to contents

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 columns:

  • time Time value from Clampfit which is in milliseconds x 10. For example, 5 seconds = 50000 in this column.

  • 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.

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.

Examples


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