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

``` {r, echo = FALSE} knitr::opts_chunk$set(eval = FALSE)

This vignette should serve as a supplement to the Get Started vignette (`vignette("scdrake")`) and
expects you have finished the initial three steps.

Other "hot" topics and questions can be found in `vignette("scdrake_faq)`

***

## Retrieving intermediate results (targets)

In `{drake}`'s terminology, a pipeline is called *plan*, and is composed of *targets*. When a target is finished,
its value (object) is saved to cache (the directory `.drake` by default). The cache has two main purposes:

- If a target is not changed, its value is loaded from the cache. *Change* involves e.g. target's definition (code) or
  change in upstream targets on which the target depends. This way `{drake}` is able to skip computation of finished
  targets and greatly enhance the runtime. More details [here](https://books.ropensci.org/drake/triggers.html).
- Users also have access to the cache, and so you can load any finished target into your R session.

Users can access the cache via two `{drake}`'s functions:

- `drake::loadd()` loads target's value to the current session as a variable of the same name.
- `drake::readd()` returns target's value (so it can be assigned to variable).

Let's try it and load the filtered `SingleCellExperiment` object:

```r
drake::loadd(sce_final_input_qc)

Value of the target sce_final_input_qc was loaded as a variable of the same name to your current R session (or more precisely, to the global environment).

Similarly, we can load this target to a variable of our choice:

sce <- drake::readd(sce_final_input_qc)

And work further with the loaded object, e.g.

scater::plotExpression(sce, "NOC2L", exprs_values = "counts", swap_rownames = "SYMBOL")

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How to dig into scdrake plans?

For a more schematic overview of pipelines and stages see vignette("pipeline_overview"), where are also diagrams.

Advanced users might be interested in looking into source code of {scdrake}'s plans (files named plans_*.R).

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Running the pipeline in parallel mode

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Using an alternative storage format (qs)

By default, R's Rds format is used (see ?saveRds) to save intermediate results to {drake}s cache, but instead, we recommend to use DRAKE_FORMAT: "qs" (see https://github.com/traversc/qs) in config/pipeline.yaml that offers better performance, but sometimes doesn't work correctly (drake throws untraceable errors).

See https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets for more details.

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Extending the pipeline

See vignette("scdrake_extend"), please.

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