Information about sex, age, treatment, and animal ID
Source:R/Sample-datasets.R
sample_cell_characteristics.RdThis dataset provides an example of the type of cell characteristics that you should be recording for your data. The dataset contains columns for the animal number, age, sex, the synapses being recorded from, and treatments applied. There is also a column for access, which is stored as a list.
The most important column is letter. This is a unique identifier that
you will assign to each recording. The letter column will enable you to
link all information relevant to the recording (evoked current data,
spontaneous current data, animal data like age, sex, etc.) from different
files.
You should import this .csv file using the import_cell_characteristics_df()
function, which will format it in a format that makes it easy to merge with
raw recording data in functions like make_normalized_EPSC_data(). This will
enable you to analyze relationships between properties like age and current
amplitude.
Format
A dataframe with 19 rows and 14 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. Example: "A"
- cell
A character or numeric value representing the cell. For example, use
3.1.1for animal #3, slice #1, cell #1.- sex
A character value such as
"Male"or"Female".- X
A numeric value representing the x-value of the cell's location in µm.
- Y
A numeric value representing the y-value of the cell's location in µm.
- 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). Do not use characters (e.g. avoid "P31" and use 31 instead).
- animal
A numeric value representing the animal's ID or number.
- synapses
A character value such as "Glutamate" or "GABA".
- treatment
A character value such as "Control" or "HNMPA".
- category
A numeric value representing the experiment type. Used to assign top-level groups for further analyses, with
treatmentas 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.- R_a
A list of values for the access resistance, which would have been monitored at several timepoints throughout the recording. See the section
R_aformatting in the documentation forimport_cell_characteristics_df().- notes
An optional character column with notes about any issues, sweeps that were removed during Clampfit processing, etc.
- 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.).
See also
import_cell_characteristics_df() to import data like this from a
.csv file.
make_interactive_summary_table() for a function which merges cell
characteristics information with pruned evoked and spontaneous current data
to create an interactive overview table of all recordings.
Examples
utils::read.csv(import_ext_data("sample_cell_characteristics.csv"))
#> letter cell sex X Y age animal synapses treatment
#> 1 BN 25.1.2 Male 152.92125 337.1888 29 25.0 Glutamate Control
#> 2 AZ 21.1.1 Female 352.61800 331.7375 32 21.0 Glutamate Control
#> 3 AO 17.1.1 Male NA NA 39 17.0 Glutamate Control
#> 4 BO 27.2.1 Male NA NA 32 27.0 Glutamate HNMPA
#> 5 BT 30.2.1 Male 387.19250 586.9837 37 30.0 Glutamate HNMPA
#> 6 CG 35.1.3 Female 164.18000 366.5200 36 35.0 Glutamate HNMPA
#> 7 L 8.5.2.1 Male NA NA 38 8.5 Glutamate Control
#> 8 CZ 41.2.2 Male 296.51000 492.9000 28 41.0 Glutamate HNMPA
#> 9 FT 72.2.1 Female 153.33000 337.1800 39 72.0 Glutamate HNMPA
#> 10 FX 74.1.2 Female 234.69000 495.5000 28 74.0 Glutamate PPP
#> 11 GF 77.3.1 Female 217.23000 323.5500 36 77.0 Glutamate PPP
#> 12 GI 81.1.1 Female 235.96000 284.2300 28 81.0 Glutamate PPP
#> 13 GK 84.1.1 Male 248.74000 574.4400 35 84.0 Glutamate PPP
#> 14 GR 90.3.1 Male 313.50000 415.9700 34 90.0 Glutamate PPP
#> 15 GX 97.2.3 Male NA NA 33 97.0 Glutamate PPP_and_HNMPA
#> 16 HB 100.1.1 Male 133.20000 590.2500 39 100.0 Glutamate PPP_and_HNMPA
#> 17 HC 100.2.2 Male 172.54000 576.2600 39 100.0 Glutamate PPP_and_HNMPA
#> 18 HG 103.2.1 Female NA NA 34 103.0 Glutamate PPP_and_HNMPA
#> 19 HN 109.1.1 Male 288.97000 400.1800 38 109.0 Glutamate PPP_and_HNMPA
#> 20 AV 20.3.1 Female 55.09656 248.8031 31 20.0 Glutamate Control
#> category R_a notes days_alone
#> 1 2 1.6, 1.7, 1.7, 1.8, 1.9, 2.0 NA 0
#> 2 2 2.5, 2.5, 2.6, 2.6, 2.9, 2.6, 2.6, 2.6, 2.7 NA 0
#> 3 2 1.9, 1.9, 1.8, 1.9, 2.0, 3.0 NA 1
#> 4 2 1.7, 1.7, 1.7, 1.8, 1.7, 1.8 NA 0
#> 5 2 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.8, 1.5, 1.5, 1.5 NA 0
#> 6 2 2.0, 2.1, 2.1, 2.2, 2.2, 2.2 NA 0
#> 7 2 1.4, 1.5, 1.5, 1.6, 1.6, 1.5 NA 0
#> 8 2 2.0, 2.0, 2.1, 2.2, 2.1, 2.1 NA 0
#> 9 2 1.5, 1.5, 1.6, 1.7, 1.9,, 2.0 NA 1
#> 10 2 1.8, 1.9, 2.1, 2.0, 2.3 NA 0
#> 11 2 1.6, 1.6, 1.7, 1.7, 1.8, 1.7 NA 0
#> 12 2 1.3, 1.3, 1.3, 1.3, 1.4, 1.4 NA 0
#> 13 2 2.2, 2.2, 2.2, 2.3, 2.5 NA 0
#> 14 2 1.3, 1.4, 1.5, 1.5, 1.6, 1.8 NA 0
#> 15 2 1.6, 1.6, 1.7, 1.7, 1.8, 1.7 NA 1
#> 16 2 2.2, 2.5, 2.5, 2.6, 2.6, 2.6 NA 2
#> 17 2 1.4, 1.5, 1.6, 1.9, 1.8, 2.3 NA 2
#> 18 2 1.7, 1.7, 1.7, 1.6 NA 0
#> 19 2 1.7, 1.7, 1.7, 1.7, 1.7, 1.7 NA 0
#> 20 2 1.6, 1.8, 1.8, 2.0, 2.0, 2.0 NA 0
#> animal_or_slicing_problems
#> 1 no
#> 2 no
#> 3 no
#> 4 no
#> 5 no
#> 6 no
#> 7 no
#> 8 no
#> 9 no
#> 10 no
#> 11 no
#> 12 no
#> 13 yes
#> 14 no
#> 15 yes
#> 16 yes
#> 17 yes
#> 18 no
#> 19 yes
#> 20 no