getStatsIntervals: Compute credible intervals for rhythm or differential rhythm...

In hugheylab/limorhyde2: Quantify Rhythmicity and Differential Rhythmicity in Genomic Data

Compute credible intervals for rhythm or differential rhythm statistics

Description

This function uses posterior samples to quantify uncertainty in the properties of fitted curves.

Usage

getStatsIntervals(posteriorStats, mass = 0.9, method = c("eti", "hdi"))

Arguments

posteriorStats	A data.table of statistics for posterior samples, as returned by getRhythmStats() or getDiffRhythmStats().
mass	Number between 0 and 1 indicating the probability mass for which to calculate the intervals.
method	String indicating the type of interval: 'eti' for equal-tailed using stats::quantile(), or 'hdi' for highest density using HDInterval::hdi().

Value

A data.table containing lower and upper bounds of various statistics for each feature or each feature-condition pair. For peak_trough_amp and rms_amp, a negative lower bound indicates a rhythm of the opposite phase.

See Also

getRhythmStats(), getDiffRhythmStats(), getExpectedMeasIntervals()

Examples

library('data.table')

y = GSE54650$y
metadata = GSE54650$metadata

fit = getModelFit(y, metadata)
fit = getPosteriorFit(fit)
fit = getPosteriorSamples(fit, nPosteriorSamples = 10L)

rhyStatsSamps = getRhythmStats(
  fit, features = c('13170', '13869'), fitType = 'posterior_samples')
rhyStatsInts = getStatsIntervals(rhyStatsSamps)

hugheylab/limorhyde2 documentation built on Jan. 29, 2024, 8:36 p.m.