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Evoked current data summarized into 5-minute intervals

Source: R/Sample-datasets.R
sample_summary_eEPSC_df.Rd

This is an example of the summary eEPSC data produced using make_summary_EPSC_data(). It is useful for demonstrating functions that build off of this dataset, such as plot_summary_current_data(). This is a list of three dataframes.

Format

An .rda file containing a list of three dataframes. The first dataframe ($percent_change_data) contains the mean current amplitude for each interval, with a final column (percent_change) containing the final percent change in amplitude in the last interval relative to the baseline interval. The second dataframe ($summary_data) contains summary statistics for each interval. The third dataframe ($mean_SE) contains averaged evoked current amplitudes (with standard error) for each time interval. This is useful for publications where you want to report your findings as means +/- SE or SD.

See below for more details.

$percent_change_data

category

A factor representing the experiment type. Used to assign top-level groups for further analyses, with treatment as subgroups. For example, "1" may refer to an experiment where you applied high-frequency stimulation (HFS) to a cell, while "2" is an experiment where you added a hormone like leptin. "3" may be an experiment where you applied HFS in the continuous presence of leptin.

letter

A factor that is a unique identifier for a single recording. Used to link data sets for evoked or spontaneous currents and cell-characteristics.

sex

A factor with two levels (e.g. "Male" or "Female").

treatment

A factor based on the treatment applied (e.g. "Control", "HNMPA"). This represents the antagonists or agonists applied, or any protocol applied to the animals (e.g. "Fasting").

age

A numeric value representing the animal's age. Can be any value as long as the time units are consistent throughout (e.g. don't mix up days and months when reporting animal ages).

animal

A numeric value representing the animal's ID or number.

X

A numeric value representing the x-value of the cell's location in µm. Leave this blank if you don't have this data.

Y

A numeric value representing the y-value of the cell's location in µm. Leave this blank if you don't have this data.

synapses

A character value (e.g. "Glutamate" or "GABA").

days_alone

A numeric value describing the number of days that the animal was left alone in a cage. This typically ranges from 0 to 2. Fasted animals will have 1 day alone.

animal_or_slicing_problems

A character value ("yes" or "no") describing if there were any issues with the animal (for example, the animal was unusually anxious) or slicing (there were delays during the process, the slices were crumpling, etc.).

t0to5

The mean evoked current amplitude (pA) for this cell during the period of 0 to 5 minutes.

t5to10

The mean evoked current amplitude (pA) for this cell during the period of 5 to 10 minutes.

t10to15, t15to20, tXtY etc...

The mean evoked current amplitude (pA) for this cell during the period of X to Y minutes.

percent_change

The percent change in evoked current amplitude in the interval t20to25 as a percentage of the mean baseline amplitude (t0to5). For example, if currents began at 100 pA during the baseline period, but were 50 pA by t20to25, the value of percent_change will be 50% or 0.50.

$summary_data

category

A factor representing the experiment type. Used to assign top-level groups for further analyses, with treatment as subgroups. For example, "1" may refer to an experiment where you applied high-frequency stimulation (HFS) to a cell, while "2" is an experiment where you added a hormone like leptin. "3" may be an experiment where you applied HFS in the continuous presence of leptin.

letter

A factor that is a unique identifier for a single recording. Used to link data sets for evoked or spontaneous currents and cell-characteristics.

sex

A factor with two levels (e.g. "Male" or "Female").

treatment

A factor based on the treatment applied (e.g. "Control", "HNMPA"). This represents the antagonists or agonists applied, or any protocol applied to the animals (e.g. "Fasting").

interval

A factor indicating the interval that the data point belongs to. For example, interval will be "t0to5" for any data points from 0 to 5 minutes. Example values: "t0to5", "t5to10", etc.

mean_P1_transformed

A numeric value representing the mean current amplitude (in pA normalized to the baseline amplitude) of the first evoked current. The values used to produce mean_P1_transformed come from all data points within each interval (the length of the interval was specified in make_normalized_EPSC_data()).

mean_P1_raw

The same values as those in mean_P1_transformed except these values contain raw values for current amplitude (e.g. the data were not baseline transformed).

n

The number of data points used to produce each value in mean_P1_transformed and mean_P1_raw

sd

The standard deviation of the mean current values.

cv

The coefficient of variation of the mean current values.

se

The standard error of the mean current values.

cv_inverse_square

The inverse coefficient of variation squared of the mean current values. Calculated by using (1/cv^2), where cv is the coefficient of variation. Useful for variance analysis.

variance

The variance of the current values, calculated using stats::var().

VMR

The variance-to-mean ratio, calculated using variance/mean_P1_transformed. Useful for variance analysis.

age

A numeric value representing the animal's age. Can be any value as long as the time units are consistent throughout (e.g. don't mix up days and months when reporting animal ages).

animal

A numeric value representing the animal's ID or number.

X

A numeric value representing the x-value of the cell's location in µm. Leave this blank if you don't have this data.

Y

A numeric value representing the y-value of the cell's location in µm. Leave this blank if you don't have this data.

time

A numeric value that represents time in minutes. This column is autogenerated in add_new_cells().

synapses

A character value (e.g. "Glutamate" or "GABA").

days_alone

A numeric value describing the number of days that the animal was left alone in a cage. This typically ranges from 0 to 2. Fasted animals will have 1 day alone.

animal_or_slicing_problems

A character value ("yes" or "no") describing if there were any issues with the animal (for example, the animal was unusually anxious) or slicing (there were delays during the process, the slices were crumpling, etc.).

$mean_SE

  • category The experiment category (please see import_cell_characteristics_df() for more details).

  • sex The sex of the animal

  • treatment The treatment applied.

  • n The number of data points (i.e. cells)

  • mean_baseline_raw_P1 The average evoked current amplitude (taken from mean_P1_raw) during the baseline_interval.

  • sd_baseline_raw_P1 The standard deviation of mean_baseline_raw_P1.

  • se_baseline_raw_P1 The standard error of mean_baseline_raw_P1. Taken by dividing sd_baseline_raw_P1 by the square root of n.

  • mean_ending_raw_P1 The average evoked current amplitude (taken from mean_P1_raw) during the ending_interval.

  • sd_ending_raw_P1 The standard deviation of mean_ending_raw_P1.

  • se_ending_raw_P1 The standard error of mean_ending_raw_P1. Taken by dividing sd_ending_raw_P1 by the square root of n.

  • VMR The variance-to-mean ratio (VMR) of P1_transformed.

  • interval A character value indicating the interval that the data point belongs to. For example, interval will be "t0to5" for any data points from 0 to 5 minutes. Example values: "t0to5", "t5to10", etc.

  • letter, synapses, sex, treatment, etc. Unmodified columns from the original dataset describing the cell's properties.

See also

make_normalized_EPSC_data() and make_pruned_EPSC_data()