get_plan: Get a 'drake' plan for a specific analysis type.

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

Get a drake plan for a specific analysis type.

Description

These functions are internally loading and binding a smaller plans (subplans) into full plans. All of them are using get_common_subplan(), get_cluster_markers_subplan(), and get_contrasts_subplan().

get_single_sample_plan() uses get_input_qc_subplan() and get_norm_clustering_subplan().

get_integration_plan() uses get_integration_subplan() and get_int_clustering_subplan().

Usage

get_single_sample_plan(cfg, cfg_pipeline = NULL)

get_integration_plan(cfg, cfg_pipeline = NULL)

Arguments

cfg	For get_single_sample_plan(): A list of config lists returned by load_single_sample_configs(). For get_integration_plan(): A list of config lists returned by load_integration_configs().
cfg_pipeline	One of: A scdrake_list object: pipeline config (see load_pipeline_config()) obtained from pipeline.yaml file located in a pipeline config directory NULL: the config will be loaded using the path defined in the scdrake_pipeline_config_dir option

Value

drake::drake_plan()

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.