ECoGRepository: R6 class for 'iEEG/ECoG' data Repository

In beauchamplab/rave: R Analysis and Visualization of 'ECOG/iEEG' Data

R6 class for iEEG/ECoG data Repository

Description

A repository to keep subject information, including electrode instances, reference information, epoch data, and offers method to epoch data.

Public fields

subject

Subject instance

raw

dictionary to store Electrode instances

reference

dictionary to store references for electrodes

epochs

dictionary to store epoch data

raw_volt

environment, stores pre-referenced analog traces

raw_power

environment, stores pre-referenced power spectrum

raw_phase

environment, stores pre-referenced phase data

volt

environment, stores referenced analog traces

power

environment, stores referenced power spectrum

phase

environment, stores referenced phase data

Methods

Public methods

• ECoGRepository$info()

• ECoGRepository$print()

• ECoGRepository$new()

• ECoGRepository$get_electrode()

• ECoGRepository$load_electrodes()

• ECoGRepository$epoch()

• ECoGRepository$load_reference()

• ECoGRepository$baseline()

---

Method info()

obtain the information

Usage

ECoGRepository$info(print = TRUE)

Arguments

print

logical, whether to print the information, default is true

Returns

character of the information

---

Method print()

print memory address

Usage

ECoGRepository$print(...)

Arguments

...

ignored

Returns

none

---

Method new()

constructor

Usage

ECoGRepository$new(subject, reference = "default", autoload = TRUE)

Arguments

subject

character such as "project/subject" or Subject instance

reference

character, reference name, default is "default", which refers to "reference_default.csv" in subject meta folder

autoload

logical, whether to auto-load reference for all electrodes, default is yes.

Returns

An ECoGRepository instance

---

Method get_electrode()

get Electrode instances

Usage

ECoGRepository$get_electrode(electrode, name = "raw")

Arguments

electrode

integers, referring to electrode numbers

name

character, "raw", "power", "raw_phase", etc.

Returns

list of environments containing electrode instances

---

Method load_electrodes()

load electrodes; usually don't need to directly call this method if autoload is true when initializing the repository

Usage

ECoGRepository$load_electrodes(electrodes, reference = "default")

Arguments

electrodes

electrode number (integer)

reference

name of reference

Returns

none

---

Method epoch()

slice the data according to epoch table

Usage

ECoGRepository$epoch(
  epoch_name,
  pre,
  post,
  electrodes = NULL,
  frequency_range = NULL,
  data_type = "power",
  referenced = TRUE,
  func = NULL,
  quiet = FALSE
)

Arguments

epoch_name

the name of epoch; for example, "YABa" refers to "epoch_YABa.csv" in subject meta folder.

pre

positive number in seconds, how long should the time be kept before the onset

post

positive number in seconds, how long should the time be kept after onset

electrodes

integers, electrode numbers

frequency_range

experimental, frequency range to include

data_type

data types to epoch; default is "power", which is power spectrum, or amplitude. Other choices are "phase" for phase data and "volt" for voltage or analog signal traces.

referenced

whether to load data referenced or without reference

func

experimental, function to apply to each electrodes

quiet

whether to suppress output messages, default is no

Returns

none. However the results are stored in public fields.

---

Method load_reference()

load references

Usage

ECoGRepository$load_reference(ref_name, electrodes = NULL)

Arguments

ref_name

reference name

electrodes

electrode numbers

Returns

none

---

Method baseline()

baseline signals (deprecated)

Usage

ECoGRepository$baseline(from, to, electrodes = NULL, print.time = FALSE)

Arguments

from, to, electrodes, print.time

internally used

Returns

data after baseline. Please use baseline instead

Author(s)

Zhengjia Wang

Examples

## Not run: 

# Two ways to create instances
repo <- ECoGRepository$new('demo/YAB')

subject <- Subject$new(project_name = 'demo', subject_code = 'YAB')
repo <- ECoGRepository$new(subject)

# Create an instance without auto collecting references, only load 
# interesting electrodes
repo <- ECoGRepository$new('demo/YAB', autoload = FALSE)
repo$load_electrodes(c(14,15))

# Create an instance with non-default reference
repo <- ECoGRepository$new('demo/YAB', reference = 'bipolar')

# Epoch data according to epoch file "epoch_YABaOutlier.csv" in meta folder
# epoch_name should be "epoch_(name).csv"
repo$epoch(epoch_name = 'YABaOutlier', pre = 1, post = 2, 
           electrodes = 14, referenced = TRUE, data_type = "power")
repo$power
#> Dimension:  287 x 16 x 301 x 1 
#> - Trial: 1, 2, 3, 4, 5, 6,...
#> - Frequency: 2, 12, 22, 32, 42...
#> - Time: -1, -0.99, -0.98,...
#> - Electrode: 14


## End(Not run)

beauchamplab/rave documentation built on Feb. 16, 2025, 8:12 p.m.