R: Prepare SCE for DS analysis

prepSCE {muscat}

R Documentation

Prepare SCE for DS analysis

Description

...

Usage

prepSCE(x, cluster_id, sample_id, group_id, drop = FALSE)

Arguments

`x`	a `SingleCellExperiment`.
`cluster_id, sample_id, group_id`	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
counts <- matrix(sample(ng * nc), nrow = ng, ncol = nc)
    
# 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)

# construct SCE
library(SingleCellExperiment)
sce <- SingleCellExperiment(
  assays = list(counts = counts),
  colData = data.frame(group = gids, id = sids, cluster = kids, batch))
    
# prep. for workflow
sce <- prepSCE(sce,
  group_id = "group",
  sample_id = "id", 
  cluster_id = "cluster")
    
head(colData(sce))
metadata(sce)$experiment_info

[Package muscat version 1.0.1 Index]