data {muscat} | R Documentation

## Example datasets

### Description

A `SingleCellExperiment` containing 10x droplet-based scRNA-seq PBCM data from 8 Lupus patients befor and after 6h-treatment with INF-beta (16 samples in total).

The original data has been filtered to

- remove unassigned cells & cell multiplets

- retain only 4 out of 8 samples per experimental group

- retain only 5 out of 8 subpopulations (clusters)

- retain genes with a count > 1 in > 50 cells

- retain cells with > 200 detected genes

- retain at most 100 cells per cluster-sample instance

Assay `logcounts` corresponds to log-normalized values obtained from `logNormCounts` with default parameters.

The original measurement data, as well as gene and cell metadata is available through the NCBI GEO accession number GSE96583; code to reproduce this example dataset from the original data is provided in the examples section.

### Value

a `SingleCellExperiment`.

### Author(s)

Helena L Crowell

### References

Kang et al. (2018). Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nature Biotechnology, 36(1): 89-94. DOI: 10.1038/nbt.4042.

### Examples

    ## Not run:
    # set random seed for cell sampling
    set.seed(2929)

    # load data
    library(ExperimentHub)
    eh <- ExperimentHub()
    sce <- eh[["EH2259"]]

    # drop unassigned cells & multiplets
    sce <- sce[, !is.na(sce$cell)]
    sce <- sce[, sce$multiplets == "singlet"]

    # keep 4 samples per group
    sce$id <- paste0(sce$stim, sce$ind)
    inds <- sample(sce$ind, 4)
    ids <- paste0(levels(sce$stim), rep(inds, each = 2))
    sce <- sce[, sce$id %in% ids]

    # keep 5 clusters
    kids <- c("B cells", "CD4 T cells", "CD8 T cells",
        "CD14+ Monocytes", "FCGR3A+ Monocytes")
    sce <- sce[, sce$cell %in% kids]
    sce$cell <- droplevels(sce$cell)

    # basic filtering on  genes & cells
    gs <- rowSums(counts(sce) > 1) > 50
    cs <- colSums(counts(sce) > 0) > 200
    sce <- sce[gs, cs]

    # sample max. 100 cells per cluster-sample
    cs_by_ks <- split(colnames(sce), list(sce$cell, sce$id))
    cs <- sapply(cs_by_ks, function(u)
        sample(u, min(length(u), 100)))
    sce <- sce[, unlist(cs)]

    # compute logcounts
    library(scater)
    sce <- computeLibraryFactors(sce)
    sce <- logNormCounts(sce)

    # re-format for 'muscat'
    sce <- prepSCE(sce,
        cluster_id = "cell",
        sample_id = "id",
        group_id = "stim",
        drop = TRUE)

    ## End(Not run)

[Package muscat version 1.4.0 Index]