Run FFT-NLLS period analysis on a fluorescence trace matrix

Usage

computePeriod(
  df,
  excludeNC = FALSE,
  top = 30,
  bottom = 18,
  save.trace = FALSE,
  rm.start = 0,
  prep_tbl = TRUE,
  preprocess = TRUE,
  transp = TRUE,
  add_t = TRUE,
  time_res = 0.5,
  smooth = TRUE,
  invert = FALSE,
  filterRAE = NULL,
  ...
)

Arguments

df: Numeric matrix or data frame of fluorescence traces (cells × frames), or a long-format table if prep_tbl = FALSE.
excludeNC: Logical; if TRUE, excludes non-circadian cells from the returned table. Defaults to FALSE.
top: Numeric; upper period bound in hours. Defaults to 30.
bottom: Numeric; lower period bound in hours. Defaults to 18.
save.trace: Logical; whether to store individual fitted traces. Defaults to FALSE.
rm.start: Integer; number of initial time points to discard before analysis. Defaults to 0.
prep_tbl: Logical; if TRUE, calls prep_table() to reshape df before analysis. Defaults to TRUE.
preprocess: Logical; if TRUE, smooths and detrends traces during table preparation. Defaults to TRUE.
transp: Logical; if TRUE, transposes df during table preparation. Defaults to TRUE.
add_t: Logical; if TRUE, adds a time column during table preparation. Defaults to TRUE.
time_res: Numeric; temporal resolution in hours per frame. Defaults to 0.5.
smooth: Logical; if TRUE, uses the smoothed trace for analysis. Defaults to TRUE.
invert: Logical; if TRUE, inverts the fluorescence signal before analysis. Defaults to FALSE.
filterRAE: Numeric threshold for the Relative Amplitude Error; cells with RAE above this value are excluded. Pass NULL to disable filtering. Defaults to NULL.
...: Currently unused.

Value

A named list with elements period_table (data frame of per-cell results), period_table_unfiltered, and optionally traces and fit_traces.