simData {muscat} | R Documentation

## simData

### Description

Simulation of complex scRNA-seq data

### Usage

    simData(
      x,
      nc = 2000,
      ns = 3,
      nk = 3,
      probs = NULL,
      p_dd = diag(6)[1, ],
      paired = FALSE,
      p_ep = 0.5,
      p_dp = 0.3,
      p_dm = 0.5,
      p_type = 0,
      lfc = 2,
      rel_lfc = NULL,
      phylo_tree = NULL,
      phylo_pars = c(ifelse(is.null(phylo_tree), 0, 0.1), 3),
      ng = nrow(x),
      force = FALSE
    )

### Arguments

`x` | a `SingleCellExperiment`.
`nc, ns, nk` | # of cells, samples and clusters to simulate.
`probs` | a list of length 3 containing probabilities of a cell belonging to each cluster, sample, and group, respectively. List elements must be NULL (equal probabilities) or numeric values in [0, 1] that sum to 1.
`p_dd` | numeric vector of length 6. Specifies the probability of a gene being EE, EP, DE, DP, DM, or DB, respectively.
`paired` | logical specifying whether a paired design should be simulated (both groups use the same set of reference samples) or not (reference samples are drawn at random).
`p_ep, p_dp, p_dm` | numeric specifying the proportion of cells to be shifted to a different expression state in one group (see details).
`p_type` | numeric. Probability of EE/EP gene being a type-gene. If a gene is of class "type" in a given cluster, a unique mean will be used for that gene in the respective cluster.
`lfc` | numeric value to use as mean logFC (logarithm base 2) for DE, DP, DM, and DB type of genes.
`rel_lfc` | numeric vector of relative logFCs for each cluster. Should be of length `nlevels(x$cluster_id)` with `levels(x$cluster_id)` as names. Defaults to factor of 1 for all clusters.
`phylo_tree` | newick tree text representing cluster relations and their relative distance. An explanation of the syntax can be found here. The distance between the nodes, except for the original branch, will be translated in the number of shared genes between the clusters belonging to these nodes (this relation is controlled with `phylo_pars`). The distance between two clusters is defined as the sum of the branches lengths separating them.
`phylo_pars` | vector of length 2 providing the parameters that control the number of type genes. Passed to an exponential PDF (see details).
`ng` | # of genes to simulate. Importantly, for the library sizes computed by `prepSim` (= `exp(x$offset)`) to make sense, the number of simulated genes should match with the number of genes in the reference. To simulate a reduced number of genes, e.g. for testing and development purposes, please set `force = TRUE`.
`force` | logical specifying whether to force simulation despite `ng != nrow(x)`.

### Details

`simData` simulates multiple clusters and samples across 2 experimental conditions from a real scRNA-seq data set.

The simulation of type genes can be performed in 2 ways; (1) via `p_type` to simulate independant clusters, OR (2) via `phylo_tree` to simulate a hierarchical cluster structure.

For (1), a subset of `p_type` % of genes are selected per cluster to use a different references genes than the remainder of clusters, giving rise to cluster-specific NB means for count sampling.

For (2), the number of shared/type genes at each node are given by `a*G*e^(-b*d)`, where

- `a` – controls the percentage of shared genes between nodes. By default, at most 10% of the genes are reserved as type genes (when `b` = 0). However, it is advised to tune this parameter depending on the input `prep_sce`.

- `b` – determines how the number of shared genes decreases with increasing distance d between clusters (defined through `phylo_tree`).

### Value

a `SingleCellExperiment` containing multiple clusters & samples across 2 groups as well as the following metadata:

cell metadata (`colData(.)`)

  a `DataFrame` containing, containing, for each cell, it's cluster, sample, and group ID.

gene metadata (`rowData(.)`)

  a `DataFrame` containing, for each gene, it's `class` (one of "state", "type", "none") and specificity (`specs`; NA for genes of type "state", otherwise a character vector of clusters that share the given gene).

experiment metadata (`metadata(.)`)
  `experiment_info`

    a `data.frame` summarizing the experimental design.

  `n_cells`

    the number of cells for each sample.

  `gene_info`

    a `data.frame` containing, for each gene in each cluster, it's differential distribution `category`, mean `logFC` (NA for genes for categories "ee" and "ep"), gene used as reference (`sim_gene`), dispersion `sim_disp`, and simulation means for each group `sim_mean.A/B`.

  `ref_sids/kidskids`

    the sample/cluster IDs used as reference.

  `args`

    a list of the function call's input arguments.

### Author(s)

Helena L Crowell & Anthony Sonrel

### References

Crowell, HL, Soneson, C, Germain, P-L, Calini, D, Collin, L, Raposo, C, Malhotra, D & Robinson, MD: On the discovery of population-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data. bioRxiv 713412 (2018). doi: https://doi.org/10.1101/713412

### Examples

    data(sce)
    library(SingleCellExperiment)

    # prep. SCE for simulation
    ref <- prepSim(sce)

    # simulate data
    (sim <- simData(ref, nc = 200,
      p_dd = c(0.9, 0, 0.1, 0, 0, 0),
      ng = 100, force = TRUE,
      probs = list(NULL, NULL, c(1, 0))))

    # simulation metadata
    head(gi <- metadata(sim)$gene_info)

    # should be ~10% DE
    table(gi$category)

    # unbalanced sample sizes
    sim <- simData(ref, nc = 100, ns = 2,
      probs = list(NULL, c(0.25, 0.75), NULL),
      ng = 10, force = TRUE)
    table(sim$sample_id)

    # one group only
    sim <- simData(ref, nc = 100,
      probs = list(NULL, NULL, c(1, 0)),
      ng = 10, force = TRUE)
    levels(sim$group_id)

    # HIERARCHICAL CLUSTER STRUCTURE
    # define phylogram specifying cluster relations
    phylo_tree <- "(('cluster1':0.1,'cluster2':0.1):0.4,'cluster3':0.5);"
    # verify syntax & visualize relations
    library(phylogram)
    plot(read.dendrogram(text = phylo_tree))

    # let's use a more complex phylogeny
    phylo_tree <- "(('cluster1':0.4,'cluster2':0.4):0.4,('cluster3':
      0.5,('cluster4':0.2,'cluster5':0.2,'cluster6':0.2):0.4):0.4);"
    plot(read.dendrogram(text = phylo_tree))

    # simulate clusters accordingly
    sim <- simData(ref,
      phylo_tree = phylo_tree,
      phylo_pars = c(0.1, 3),
      ng = 500, force = TRUE)
    # view information about shared 'type' genes
    table(rowData(sim)$class)

[Package muscat version 1.4.0 Index]