sce_int_import_fn: Import 'sce_final_norm_clustering' targets from 'drake'...

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Import sce_final_norm_clustering targets from drake caches.

Description

SingleCellExperiment objects are also checked for common HVG metric, and HVG combination method is validated.

Usage

sce_int_import_fn(
  integration_sources,
  hvg_combination = c("hvg_metric", "intersection", "union", "all")
)

Arguments

integration_sources	A list of sources to load sce_final_norm_clustering targets from. See ⁠01_integration.yaml⁠ config for more details.
hvg_combination	A character scalar: method to use for combining HVGs: "hvg_metric": combine gene variance or CV2, e.g. all samples had HVG_METRIC set to "gene_var"(scran::combineVar()) or "gene_cv2" (scran::combineCV2()). "intersection": make intersection of HVGs. "union": make union of HVGs. "all": take all HVGs from all samples (without duplicates).

Value

A list of SingleCellExperiment objects. Output target: sce_int_import

The following items of metadata() of each imported SingleCellExperiment object are added or modified:

• single_sample_path, single_sample_path_type, single_sample_name, single_sample_description, hvg_rm_cc_genes, hvg_cc_genes_var_expl_threshold: taken from INTEGRATION_SOURCES config parameter.

• hvg_combination: the value of the hvg_combination function argument.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.