prepSCE {muscat} | R Documentation

## Prepare SCE for DS analysis

### Description

...

### Usage

    prepSCE(
      x,
      kid = "cluster_id",
      sid = "sample_id",
      gid = "group_id",
      drop = FALSE
    )

### Arguments

`x` | a SingleCellExperiment.
`kid, sid, gid` | character strings specifying the `colData(x)` columns containing cluster assignments, unique sample identifiers, and group IDs (e.g., treatment).
`drop` | logical. Specifies whether `colData(x)` columns besides those specified as `cluster_id,sample_id,group_id` should be retained (default `drop = FALSE`) or removed (`drop = TRUE`).

### Value

a SingleCellExperiment.

### Author(s)

Helena L Crowell

### Examples

    # generate random counts
    ng <- 50
    nc <- 200

    # generate some cell metadata
    gids <- sample(c("groupA", "groupB"), nc, TRUE)
    sids <- sample(paste0("sample", seq_len(3)), nc, TRUE)
    kids <- sample(paste0("cluster", seq_len(5)), nc, TRUE)
    batch <- sample(seq_len(3), nc, TRUE)
    cd <- data.frame(group = gids, id = sids, cluster = kids, batch)

    # construct SCE
    library(scuttle)
    sce <- mockSCE(ncells = nc, ngenes = ng)
    colData(sce) <- cbind(colData(sce), cd)

    # prep. for workflow
    sce <- prepSCE(sce, kid = "cluster", sid = "id", gid = "group")
    head(colData(sce))
    metadata(sce)$experiment_info
    sce

[Package muscat version 1.6.0 Index]