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.

Value

TRUE is successful, otherwise FALSE

See Also

run_fastmnn run_harmony

hms-dbmi/drugseqr documentation built on June 24, 2024, 7:03 a.m.