discoPeriodDetection: Detect dataset-wide fits to multiple periodicities

In matthewcarlucci/DiscoRhythm: Interactive Workflow for Discovering Rhythmicity in Biological Data

Detect dataset-wide fits to multiple periodicities

Description

Detect dataset-wide fits to multiple periodicities

Usage

discoPeriodDetection(
  se,
  timeType = c("linear", "circular"),
  main_per = 24,
  test_periods = NULL
)

Arguments

se	SummarizedExperiment, the main data object used by DiscoRhythm expected to contain se$ID, se$ReplicateID, se$Time sample metadata and non-null rownames. See the vignette for more details.
timeType	character, time is either reported as "linear" or "circular" on some base-cycle (ex. time of day). This determines the periods that will be tested for.
main_per	numeric, if timeType=="circular" main_per indicates the period of the base-cycle where sampling times are derived.
test_periods	numeric, a vector of the periods to test. if timeType=="linear" and length(test_periods)==2 it will be assumed to be a range of periods to test over.

Value

A data.frame of Rsquared values for each period, for each row of Maindata.

Examples

se <- discoGetSimu(TRUE)

# Detect periods
rsqs <- discoPeriodDetection(se)

matthewcarlucci/DiscoRhythm documentation built on March 24, 2022, 10:22 a.m.