discoBatch: Core DiscoRhythm Workflow
In DiscoRhythm: Interactive Workflow for Discovering Rhythmicity in Biological Data

Description Usage Arguments Value See Also Examples

Execute the DiscoRhythm workflow with one command to obtain the results of oscillation detection (discoODAs) and optionally generate an html report with data visualizations from an Rmarkdown template. See the DiscoRhythm vignette for more details on the analysis procedures.

discoBatch(
  indata,
  report = NULL,
  outdata = TRUE,
  ncores = 1,
  timeType = "circular",
  main_per = 24,
  cor_threshold = 3,
  cor_method = "pearson",
  cor_threshType = "sd",
  pca_threshold = 3,
  pca_scale = TRUE,
  pca_pcToCut = paste0("PC", seq_len(4)),
  aov_method = "None",
  aov_pcut = 0.05,
  aov_Fcut = 0,
  avg_method = "Median",
  osc_method = NULL,
  osc_period = 24
)

`indata`	SummarizedExperiment or data.frame, see the vignette for the specific formats expected for each of these input types. `discoParseMeta`.
`report`	character, if `!is.null(report)` an html report with
`outdata`	logical, whether to return the final discoODAs (note if run with `is.null(report)` discoBatch will return nothing).
`ncores`	numeric, number of cores to use for parallelized tasks. Currently, only used in oscillation detection function `discoODAs`.
`timeType`	character, nature of the sample times provided (one of `"circular"` or `"linear"`).
`main_per`	numeric, the length of the main hypothesized period (e.g. 24hr for circadian experiments). Used in `discoPeriodDetection`.
`cor_threshold`	numeric, threshold used in inter-sample correlation analysis for outlier detection. Either in units of correlation coefficient or standard deviations from the mean (see `cor_threshType`).
`cor_method`	character, which correlation method to use for outlier removal (see cor for more details).
`cor_threshType`	character, one of "sd" or "value" indicating whether cor_threshold should be set by absolute correlation coefficient or by standard deviations from the mean of all samples.
`pca_threshold`	numeric, the number of standard deviations to set as the threshold for outlier detection in PCA outlier removal.
`pca_scale`	logical, whether to scale the data prior to PCA.
`pca_pcToCut`	character, names of which PCs to use for outlier detection (e.g. "PC1","PC2" etc.).
`aov_method`	character, method to use for ANOVA. One of: "Equal Variance", "Welch", or "None".
`aov_pcut`	numeric, p-value cutoff used to select rows with statistically significant signal-to-noise.
`aov_Fcut`	numeric, F-statistic cutoff used to select rows with high signal-to-noise based on magnitude.
`avg_method`	character, method for averaging technical replicates. One of: "Median","Mean","Random", or "None".
`osc_method`	character, vector of oscillation detection algorithms to apply to the data. Methods that are detmined to be innappropraite for the experimental design (using the `discoODAexclusionMatrix`) will be ignored. If `is.null(osc_method)` all suitable methods will be executed.
`osc_period`	numeric, a fixed period to use for oscillation detection using all methods.

returns the results of discoODAs

discoODAs, discoRepAnalysis, discoPeriodDetection, discoPCAoutliers, discoInterCorOurliers

indata <- discoGetSimu()

# Batch execute (on demo data) to generate a DiscoRhythm_report.html report.
# Returns the results of discoODAs
discoODAres <- discoBatch(indata,
report="DiscoRhythm_report.html",
osc_method="CS")