discoBatch: Core DiscoRhythm Workflow

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

Core DiscoRhythm Workflow

Description

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.

Usage

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
)

Arguments

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.

Value

returns the results of discoODAs

See Also

discoODAs, discoRepAnalysis, discoPeriodDetection, discoPCAoutliers, discoInterCorOurliers

Examples

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")

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