discoGetODAs {DiscoRhythm}R Documentation

Get Valid Oscillation Detection Algorithms

Description

Runs each selected oscillation deteciton algorithm sequentially to obtain oscillation characteristics of each row of the input data. Technical replicates are expected to be merged by this stage.

Usage

discoGetODAs(se, method = NULL, period, circular_t = FALSE)

discoODAs(se, period = 24, method = c("CS", "JTK", "LS", "ARS"),
  circular_t = FALSE, ncores = 1)

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.

method

character, short names of ODAs to use. If length>1 all input method names will be evaluated.

period

numeric, the hypothesized period to test for.

circular_t

logical, is time circular on some base-cycle (ex. time of day).

ncores

number of cores to parallelize with (applicable to JTK, ARSER and LS only). If 1 will execute in serial.

Value

A named list of results where each element is a data.frame for the corresponding method containing estimates for: p-value, amplitude, acrophase, q-value, and period used.

Examples

# Import the simulated example dataset
se <- discoCheckInput(discoGetSimu(TRUE))
# Execute the Cosinor method only
discoODAres <- discoODAs(se,method="CS")


[Package DiscoRhythm version 1.0.0 Index]