CSV/TSV I/O for PhysioExperiment

Functions for reading and writing signal data in CSV/TSV format. Supports both wide format (time x channels) and long format. Read PhysioExperiment from CSV file

Usage

readCSV(
  path,
  format = c("wide", "long"),
  time_col = NULL,
  channel_cols = NULL,
  sampling_rate = NULL,
  sep = ",",
  header = TRUE,
  ...
)

Arguments

path: Path to the CSV file.
format: Data format: "wide" (time x channels) or "long" (stacked).
time_col: Name of the time column. If NULL, assumes first column or generates time from sampling rate.
channel_cols: For wide format, column names/indices to use as channels. If NULL, uses all non-time columns.
sampling_rate: Sampling rate in Hz. Required if time column is not present.
sep: Column separator. Default is ",".
header: Logical. If TRUE, first row contains column names.
...: Additional arguments passed to read.csv/read.table.

Value

A PhysioExperiment object.

Details

Reads physiological signal data from a CSV file.

References

Wickham H (2014). "Tidy Data." Journal of Statistical Software, 59(10), 1-23. doi:10.18637/jss.v059.i10

Examples

# Write a wide-format CSV, then read it back
pe <- PhysioExperiment(
  assays = list(raw = matrix(rnorm(400), nrow = 100, ncol = 4)),
  colData = S4Vectors::DataFrame(label = c("Fz", "Cz", "Pz", "Oz")),
  samplingRate = 100
)
tmp <- tempfile(fileext = ".csv")
writeCSV(pe, tmp)

# Read using the written time column
pe_in <- readCSV(tmp, time_col = "time")

# Read without a time column (generate time from sampling rate)
pe_sr <- readCSV(tmp, channel_cols = c("Fz", "Cz", "Pz", "Oz"),
                 sampling_rate = 100)

unlink(tmp)