getPosteriorSamples: Draw samples from posterior distributions of fitted models

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

Draw samples from posterior distributions of fitted models

Description

This is an optional step in an analysis using limorhyde2, and is useful for quantifying uncertainty in posterior estimates of fitted curves and rhythmic statistics. The function calls mashr::mash_compute_posterior_matrices().

Usage

getPosteriorSamples(fit, nPosteriorSamples = 200L, overwrite = FALSE)

Arguments

fit	A ‘limorhyde2’ object containing posterior fits.
nPosteriorSamples	Number of samples to draw from each posterior distribution.
overwrite	Logical indicating whether to recompute posterior samples if they already exist.

Value

A limorhyde2 object containing everything in fit with added or updated element:

• mashPosteriorSamples: a three-dimensional array of coefficients, with dim 1 corresponding to features, dim 2 to model terms, and dim 3 to posterior samples.

See Also

getPosteriorFit(), getRhythmStats(), getExpectedMeas(), getStatsIntervals()

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.