prepSCE: Prepare SCE for DS analysis

In HelenaLC/ddSingleCell: Multi-sample multi-group scRNA-seq data analysis tools

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

HelenaLC/ddSingleCell documentation built on Oct. 14, 2024, 2:08 p.m.