tipa (version 1.0.8)

tipaCosinor: Use cosinor regression to estimate the phase shift induced by a stimulus during a circadian time-course.

Description

Calculate the phase shift based on fitting sine curves to waveform data before and after the stimulus, accounting for possible period changes and for the point in the circadian cycle at which the stimulus occurred. This function will work best for measurements whose rhythms are approximately sinusoidal, or at least smoothly increasing and decreasing. If your data are not sinusoidal, you can first define the phase reference points and then use tipaPhaseRef().

Usage

tipaCosinor(
  time,
  y,
  stimOnset,
  stimDuration = 0,
  periodGuess = 24,
  trend = TRUE,
  shortcut = TRUE
)

Value

A list.

phaseShift

Estimated phase shift in circadian hours. Negative values correspond to a delay, positive values an advance.

epochInfo

Dataframe containing information about the sine curve fits for each epoch: period (in the same units used in time), phase (in radians), and root mean square error (in the same units as y). If the RMS errors pre-stimulus and post-stimulus are substantially different, then the stimulus may have induced a change in the waveform and thus phase shift estimates may be invalid.

Arguments

time

Vector of time values for the full time-course.

y

Vector of measurements (e.g., bioluminescence) for the full time-course.

stimOnset

Time at which the stimulus started.

stimDuration

Duration of the stimulus and any transients. Data between stimOnset and stimOnset + stimDuration will be ignored.

periodGuess

Approximate period of the oscillations (in the same units used in time), used as initial value in fitting the sine curves.

trend

Model a long-term trend in the cosinor fit for each epoch. Uses a natural cubic spline with 4 degrees of freedom. It is strongly recommended to keep as TRUE. If set to FALSE, the function may give an error or give completely invalid results.

shortcut

Calculate phase shift using the standard TIPA procedure or using a shortcut based on the phases of the sine curve fits. The two methods give exactly the same result.

See Also

tipaPhaseRef()

Examples

# Time-course data from multiple (simulated) experiments
getTimecourseFile = function() {
  system.file('extdata', 'timecourses.csv', package = 'tipa')}
df = read.csv(getTimecourseFile(), stringsAsFactors = FALSE)

resultList = lapply(sort(unique(df$expId)), function(ii) {
  time = df$time[df$expId == ii]
  y = df$intensity[df$expId == ii]
  tipaCosinor(time, y, stimOnset = 0)})

phaseShifts = sapply(resultList, function(r) r$phaseShift)