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Preprocess a PSG recording

Source: R/preprocess_psg.R
preprocess_psg.Rd

Applies the standard sleep EEG preprocessing pipeline to an mrpheus_psg object: optional channel renaming, DC offset removal, powerline notch filtering (plus harmonics), and channel-type-specific bandpass filtering.

Usage

preprocess_psg(
  psg,
  channel_rename = NULL,
  dc = TRUE,
  powerline_freq = NULL,
  notch_harmonics = TRUE,
  notch_bw_hz = 2,
  eeg_bandpass = c(0.3, 35),
  eog_bandpass = c(0.3, 15),
  emg_bandpass = c(10, 99),
  ecg_bandpass = c(0.5, 40),
  verbose = TRUE
)

Arguments

psg

An mrpheus_psg object from prepare_psg().

channel_rename

Named character vector mapping old channel labels to new labels, e.g. c("C3-A2" = "C3", "O2-A1" = "O2"). Applied before filtering; updates channel_map labels accordingly. Default NULL.

dc

Logical. Remove per-channel DC offset via remove_dc(). Default TRUE.

powerline_freq

Integer or NULL. Powerline frequency in Hz (50L or 60L). NULL (default) triggers auto-detection via detect_powerline() on the first clean EEG channel.

notch_harmonics

Logical. Notch harmonics of powerline_freq up to Nyquist - 5 Hz. Default TRUE.

notch_bw_hz

Numeric. Full bandwidth of each notch in Hz. Default 2.

eeg_bandpass

Numeric vector of length 2. Bandpass limits (Hz) applied to all EEG channels. Default c(0.3, 35).

eog_bandpass

Numeric vector of length 2. Bandpass limits (Hz) applied to all EOG channels. Default c(0.3, 15).

emg_bandpass

Numeric vector of length 2. Bandpass limits (Hz) applied to all EMG channels. Default c(10, 99).

ecg_bandpass

Numeric vector of length 2. Bandpass limits (Hz) applied to all ECG channels. Default c(0.5, 40).

verbose

Logical. Print progress messages. Default TRUE.

Value

A new mrpheus_psg object with filtered signals and re-segmented epochs. The edf$signals entries are replaced in-place with the filtered continuous signals so that subsequent epoch access is consistent.

Details

Filtering is applied to the full continuous signal stored in psg$edf$signals before re-epoching, which avoids filter discontinuities at epoch boundaries. The returned object is a new mrpheus_psg with the same epoch length and channel map as the input.

The individual filter steps (remove_dc(), detect_powerline(), notch_filter(), bandpass_filter()) are exported separately and can be called on any numeric vector without constructing a PSG object.

Examples

if (FALSE) { # \dontrun{
rec  <- read_edf("data/psg_001.edf")
psg  <- prepare_psg(rec)

# Auto-detect powerline, apply standard filters
psg_clean <- preprocess_psg(psg)

# Rename linked-ear channels to 10-20 names, fix powerline explicitly
psg_clean <- preprocess_psg(
  psg,
  channel_rename = c("C3-A2" = "C3", "C4-A1" = "C4",
                     "O1-A2" = "O1", "O2-A1" = "O2"),
  powerline_freq = 50L
)
} # }