compose_channel: Compose a "phantom" channel from existing electrodes

In beauchamplab/raveio: File-System Toolbox for RAVE Project

Compose a "phantom" channel from existing electrodes

Description

In some cases, for example, deep-brain stimulation ('DBS'), it is often needed to analyze averaged electrode channels from segmented 'DBS' leads, or create bipolar contrast between electrode channels, or to generate non-equally weighted channel averages for 'Laplacian' reference. compose_channel allows users to generate a phantom channel that does not physically exist, but is treated as a normal electrode channel in 'RAVE'.

Usage

compose_channel(
  subject,
  number,
  from,
  weights = rep(1/length(from), length(from)),
  normalize = FALSE,
  force = FALSE,
  label = sprintf("Composed-%s", number),
  signal_type = c("auto", "LFP", "Spike", "EKG", "Audio", "Photodiode", "Unknown")
)

Arguments

subject	'RAVE' subject
number	new channel number, must be positive integer, cannot be existing electrode channel numbers
from	a vector of electrode channels that is used to compose this new channel, must be non-empty; see weights if these channels are not equally weighted.
weights	numerical weights used on each from channels; the length of weights must equals to the length of from; default is equally weighted for each channel (mean of from channels).
normalize	whether to normalize the weights such that the composed channel has the same variance as from channels; default is false
force	whether to overwrite existing composed channel if it exists; default is false. By specifying force=TRUE, users are risking breaking the data integrity since any analysis based on the composed channel is no longer reproducible. Also users cannot overwrite original channels under any circumstances.
label	the label for the composed channel; will be stored at 'electrodes.csv'
signal_type	signal type of the composed channel; default is 'auto' (same as the first from channel); other choices see SIGNAL_TYPES

Value

Nothing

Examples

library(raveio)


# Make sure demo subject exists in this example, just want to make
# sure the example does not error out
if(
  interactive() && "demo" %in% get_projects() &&
  "DemoSubject" %in% as_rave_project('demo')$subjects() &&
  local({
    subject <- as_rave_subject("demo/DemoSubject")
    !100 %in% subject$electrodes
  })
) {

  # the actual example code:
  # new channel 100 = 2 x channel 14 - (channe 15 + 16)
  compose_channel(
    subject = "demo/DemoSubject",
    number = 100,
    from = c(14, 15, 16),
    weights = c(2, -1, -1),
    normalize = FALSE
  )

}

beauchamplab/raveio documentation built on April 24, 2024, 11:20 p.m.