Add new data

This function enables you to append new raw recording data onto an existing datasheet. It makes it easy and convenient to merge the cell parameters (age, sex, etc.) with new data and add it to your current raw data. This function also formats the dataset so it is immediately ready for use in functions like make_normalized_EPSC_data().

Usage

add_new_cells(
  new_raw_data_csv,
  cell_characteristics_csv,
  old_raw_data_csv,
  data_type,
  software = "MiniAnalysis",
  bin_width = 5,
  write_new_csv = "yes",
  new_file_name,
  decimal_places = 2,
  injection_start_time = 265.4,
  length_of_current_injection = 0.5
)

Arguments

new_raw_data_csv: A filepath to a csv containing the new raw data. If the data are evoked current data (current_type == "eEPSC") then this must contain 4 columns: letter, ID, P1 and P2. If the data are spontaneous current data, the columns must be letter, ID, recording_num, trace, amplitude and time_of_peak. Please see the section below on required columns for more details.
cell_characteristics_csv: A filepath to a csv containing information about the cells. Please see import_cell_characteristics_df() for a description of what columns should be included. Don't forget to update this to include the cell characteristics for the new letters in new_raw_data_csv!
old_raw_data_csv: A filepath to a csv containing the current raw data. Since this function appends the new data to the old data, this must be of the same current_type as the new data (e.g. the columns must be the same). If this is the first time you are running this function, start with a blank .csv file containing just some text (e.g. letter) in cell A1. This is required because R cannot recognize an empty .csv sheet as a valid file.
data_type: A character ("eEPSC", "sEPSC", "AP_parameter" or "AP_count") describing the data type that is being imported.
software: A character ("Clampfit" or "MiniAnalysis") describing what software tool was used to analyze the data in new_raw_data_csv. This is relevant when data_type is "sEPSC" because the exported data is different. Defaults to "Clampfit".
bin_width: A numeric value (defaults to 5) describing the time interval in seconds (bin width) of the histogram used in MiniAnalysis. This is only relevant when data_type = "sEPSC" and software = "MiniAnalysis".
write_new_csv: A character ("yes" or "no") describing if the new data should be written to a csv file. Defaults to "yes". Please specify a filename for the new csv file in new_file_name.
new_file_name: A filename for the csv containing the new data appended to the old data. Must be a character representing a filepath to a csv file. Examples include "Data/20241118-Raw-eEPSC-data.csv".
decimal_places: A numeric value indicating the number of decimal places the data should be rounded to. Used to reduce file size and prevent an incorrect representation of the number of significant digits.
injection_start_time: For action potential data only: A numeric value describing the start time (in ms) when current injection was applied. Used to calculate the latency to fire.
length_of_current_injection: For action potential data only: A numeric value indicating the duration of the current injection (in s, default is 0.5 s).

Value

A dataframe consisting of the old raw data with information from the new cells appended to it. If data_type = "AP_parameter" two new columns will also be added based on calculations from the existing columns. These are latency_to_fire (which is time_to_peak - injection_start_time) and antipeak_time_relative_to_threshold (which is time_of_antipeak - time_of_threshold). If data_type = "AP_count" one new column will be added. These is AP_frequency (in Hz).

Required Columns

If the data are evoked currents (data_type = "eEPSC"), the data must contain the following four columns:

letter A character value that is a unique identifier for a single recording. Used to link data sets for evoked or spontaneous currents and cell-characteristics.
ID A character value for the recording filename.
P1 A numeric value representing the amplitude of the first evoked current in pA.
P2 A numeric value representing the amplitude of the second evoked current in pA.

If the data are spontaneous currents (data_type = "sEPSC") and these were exported from Clampfit (software = "Clampfit"), the data must contain the following columns:

letter A character value that is a unique identifier for a single recording. Used to link data sets for evoked or spontaneous currents and cell-characteristics.
ID A character value for the recording filename.
recording_num A numeric value representing the recording number. This was incorporated before we switched to concatenating all recordings into one, but it needs to remain here to prevent breaking previous projects. It should be set to 1.
trace A numeric value representing the trace (automatically generated in Clampfit) where the current occurred.
amplitude A numeric value representing the amplitude of the evoked current in pA (automatically generated in Clampfit).
time_of_peak A numeric value representing the time of the peak in milliseconds relative to trace number (automatically generated in Clampfit).

If the data are spontaneous currents (data_type = "sEPSC") and these were exported from the histogram tool in MiniAnalysis (software = "MiniAnalysis"), the data must contain the following columns:

letter A character value that is a unique identifier for a single recording. Used to link data sets for evoked or spontaneous currents and cell-characteristics.
ID A character value for the recording filename.
amplitude The average sEPSC amplitude, averaged over the time interval (bin width) that you chose for the histogram (automatically generated from histogram tool in MiniAnalysis).
SE The standard error of amplitude (automatically generated from histogram tool in MiniAnalysis).
time The time in seconds (exported automatically from the histogram, depending on the bin width that you set). add_new_cells() will automatically convert this to minutes.
num_events The number of synaptic events (sEPSCs) during the time interval (bin width). This is also automatically generated in MiniAnalysis.

If the data are action potential parameters (data_type == "AP_parameter"), the data must contain the following columns:

letter A character value that is a unique identifier for a single recording. Used to link data sets for evoked or spontaneous currents and cell-characteristics.
ID A character value for the recording filename.
state A character ("Baseline" or "Insulin") representing the timepoint that the data point belongs to.
time_of_threshold The time (in ms) when the membrane potential reaches the threshold value.
threshold The threshold (in mV). Determined using the first derivative method, where the threshold is the membrane potential which results in a derivative of 10 mV/ms or greater (Farries et al., 2010).
t_11 The value of the first derivative (action potential velocity in mV/ms) at threshold.
first_sweep_with_APs The sweep number of the first sweep (going from lowest to higher current injection values) that resulted in an action potential.
trace_start An automated value in Clampfit that is not used in the analysis.
peak_amplitude The peak amplitude (in pA) of the action potential relative to threshold.
time_to_peak The time to peak amplitude (in ms) relative to the time of threshold.
antipeak_amplitude The after-hyperpolarization amplitude (in pA) relative to threshold.
time_of_antipeak The time of the after-hyperpolarization (in ms).
half_width The half-width, which is the width of the action potential and half of the peak amplitude.

Examples



# NOTE: Remember, if you are running this for the first time,
# don't start with a blank csv for `old_raw_data_csv`.
# `old_raw_data_csv` must have at least some text
# in cell `A1` for R to recognize it.

# NOTE: If you are importing spontaneous current data from MiniAnalysis,
# don't forget to set `bin_width` to match what you used
# in the histogram tool in MiniAnalysis!

if (FALSE) { # \dontrun{
add_new_cells(
  new_raw_data_csv = "sample_new_eEPSC_data.csv",
  cell_characteristics_csv = "sample_cell_characteristics.csv",
  old_raw_data_csv = "sample_eEPSC_data.csv",
  data_type = "eEPSC",
  write_new_csv = "no",
  new_file_name = "Raw-eEPSC-Data.csv",
  decimal_places = 2
)
} # }

Usage

Arguments

Value

Required Columns

See also

Examples