sccomp_replicate: sccomp_replicate

In stemangiola/sccomp: Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

sccomp_replicate

Description

This function replicates counts from a real-world dataset.

Usage

sccomp_replicate(
  fit,
  formula_composition = NULL,
  formula_variability = NULL,
  number_of_draws = 1,
  mcmc_seed = sample(1e+05, 1)
)

Arguments

fit	The result of sccomp_estimate.
formula_composition	A formula. The formula describing the model for differential abundance, for example ~treatment. This formula can be a sub-formula of your estimated model; in this case all other factor will be factored out.
formula_variability	A formula. The formula describing the model for differential variability, for example ~treatment. In most cases, if differentially variability is of interest, the formula should only include the factor of interest as a large anount of data is needed to define variability depending to each factors. This formula can be a sub-formula of your estimated model; in this case all other factor will be factored out.
number_of_draws	An integer. How may copies of the data you want to draw from the model joint posterior distribution.
mcmc_seed	An integer. Used for Markov-chain Monte Carlo reproducibility. By default a random number is sampled from 1 to 999999. This itself can be controlled by set.seed()

Value

A tibble tbl with cell_group-wise statistics

A tibble (tbl), with the following columns:

• cell_group - A character column representing the cell group being tested.

• sample - A factor column representing the sample name from which data was generated.

• generated_proportions - A numeric column representing the proportions generated from the model.

• generated_counts - An integer column representing the counts generated from the model.

• replicate - An integer column representing the replicate number, where each row corresponds to a different replicate of the data.

Examples

message("Use the following example after having installed install.packages(\"cmdstanr\", repos = c(\"https://stan-dev.r-universe.dev/\", getOption(\"repos\")))")


  if (instantiate::stan_cmdstan_exists() && .Platform$OS.type == "unix") {
    data("counts_obj")

    sccomp_estimate(
      counts_obj,
      ~ type, ~1, sample, cell_group, count,
      cores = 1
    ) |>
    sccomp_replicate()
  }

stemangiola/sccomp documentation built on Nov. 15, 2024, 8 a.m.