Apply a pipeline to a single cell object — apply

Runs each step in order. The first step receives object; subsequent steps receive the result of the previous step. The chain is validated against the class of object before anything runs, see validate_pipeline(). Errors propagate; nothing is caught.

Usage

apply_pipeline(pipeline, object)

Arguments

pipeline: ScPipeline.
object: SingleCells, SingleCellsSubset or MetaCells. Dispatch happens inside each step's underlying generic, so the same pipeline works on any class its steps have methods for.

Value

The object after all steps have run.

Examples

# HVG then PCA, run in order on a freshly loaded object
sc <- demo_single_cells(prepped = FALSE)
p <- step_hvg_sc(hvg_no = 30L, .verbose = FALSE) %>>%
  step_pca_sc(no_pcs = 10L, .verbose = FALSE)
sc <- apply_pipeline(p, sc)
dim(get_pca_factors(sc))
#> [1] 500  10

unlink(sc@dir_data, recursive = TRUE, force = TRUE)