discoGetODAs {DiscoRhythm} | R Documentation |
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.
discoGetODAs(se, method = NULL, period, circular_t = FALSE) discoODAs(se, period = 24, method = c("CS", "JTK", "LS", "ARS"), circular_t = FALSE, ncores = 1)
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. |
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.
# Import the simulated example dataset se <- discoCheckInput(discoGetSimu(TRUE)) # Execute the Cosinor method only discoODAres <- discoODAs(se,method="CS")