Mixture-based muscle synergy analysis on PhysioExperiment objects

Thin entry point that runs muscleSynergyMixture() directly on ecosystem data: it reads each subject's time x muscle activation from a PhysioExperiment (or accepts matrices) and fits the subgroup mixture.

Usage

physioSynergyMixture(
  pe_list,
  n_clusters,
  n_factors,
  method = c("mfa", "mpca"),
  assay_name = NULL,
  ...
)

Arguments

pe_list

A list with one element per subject, each a PhysioExperiment (its assay is read) or a time x muscle matrix.

n_clusters, n_factors

Number of subgroups and synergies (factors).

method

"mfa" or "mpca" (see muscleSynergyMixture()).

assay_name

Assay to read from each PhysioExperiment (default: its default assay).

...

Further arguments passed to muscleSynergyMixture().

Value

A "synergy_mixture" object.

Examples

set.seed(1)
mk <- function(L) {
  pe <- PhysioCore::PhysioExperiment(
    assays = list(raw = t(L %*% matrix(rnorm(2 * 50), 2, 50) +
                          matrix(rnorm(6 * 50, 0, .3), 6, 50))),
    samplingRate = 100)
  pe
}
LA <- matrix(abs(rnorm(12)), 6, 2); LB <- matrix(abs(rnorm(12)), 6, 2)
pes <- c(replicate(5, mk(LA), simplify = FALSE),
         replicate(5, mk(LB), simplify = FALSE))
fit <- physioSynergyMixture(pes, n_clusters = 2, n_factors = 2, seed = 1)
fit$cluster
#>  [1] 1 1 1 1 1 2 2 2 2 2