integrate_saved_scseqs: Integrate previously saved SingleCellExperiments

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Integrate previously saved SingleCellExperiments

Description

Performs integration and saves as a new analysis. Used by explore_scseq_clusters shiny app.

Usage

integrate_saved_scseqs(
  sc_dir,
  integration_name,
  dataset_names = NULL,
  scseqs = NULL,
  integration_type = c("harmony", "fastMNN", "Azimuth", "symphony"),
  exclude_clusters = NULL,
  exclude_cells = NULL,
  subset_metrics = NULL,
  is_include = NULL,
  founder = integration_name,
  pairs = NULL,
  hvgs = NULL,
  ref_name = NULL,
  npcs = 30,
  cluster_alg = "leiden",
  resoln = 1,
  progress = NULL,
  value = 0,
  tx2gene_dir = NULL
)

Arguments

sc_dir	Directory with saved single-cell datasets.
integration_name	Name for new integrated analysis.
integration_type	Charactor vector of one or more integration types.
exclude_clusters	Charactor vector of clusters for excluding cells. Only included to save to args.
exclude_cells	Character vector of cell names to exclude.
subset_metrics	Metrics to subset based on.
is_include	Boolean - are cells that match subset_metrics included or excluded?
progress	optional Shiny Progress object.
test	Character vector of test analysis names.
ctrl	Character vector of control analysis names.

Value

TRUE is successful, otherwise FALSE

See Also

run_fastmnn run_harmony

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.