splitSwish {fishpond} | R Documentation

## Function for splitting SummarizedExperiment into separate RDS files

### Description

The `splitSwish` function splits up the `y` object along genes and writes a `Snakefile` that can be used with Snakemake to distribute running `swish` across genes. This workflow is primarily designed for large single cell datasets, and so the default is to not perform length correction within the distributed jobs. See the alevin section of the vignette for an example. See the Snakemake documention for details on how to run and customize a `Snakefile`: https://snakemake.readthedocs.io

### Usage

    splitSwish(y, nsplits, prefix = "swish", snakefile = NULL, overwrite = FALSE)

### Arguments

`y` | a SummarizedExperiment
`nsplits` | integer, how many pieces to break `y` into
`prefix` | character, the path of the RDS files to write out, e.g. `prefix="/path/to/swish"` will generate `swish.rds` files at this path
`snakefile` | character, the path of a Snakemake file, e.g. `Snakefile`, that should be written out. If `NULL`, then no `Snakefile` is written out
`overwrite` | logical, whether the `snakefile` and RDS files (`swish1.rds`, ...) should overwrite existing files

### Value

nothing, files are written out

### References

Compression and splitting across jobs:

Van Buren, S., Sarkar, H., Srivastava, A., Rashid, N.U., Patro, R., Love, M.I. (2020) Compression of quantification uncertainty for scRNA-seq counts. bioRxiv. https://doi.org/10.1101/2020.07.06.189639

Snakemake:

Koster, J., Rahmann, S. (2012) Snakemake - a scalable bioinformatics workflow engine. Bioinformatics. https://doi.org/10.1093/bioinformatics/bts480

[Package fishpond version 1.6.0 Index]