Helper function for distributing Swish on a subset of data

This function is called by the Snakefile that is generated by splitSwish. See alevin example in the vignette. As such, it doesn't need to be run by users in an interactive R session.

miniSwish(
  infile,
  outfile,
  numReps = 20,
  lengthCorrect = FALSE,
  overwrite = FALSE,
  ...
)

Arguments

infile

path to an RDS file of a SummarizedExperiment

outfile

a CSV file to write out

numReps

how many inferential replicates to generate

lengthCorrect

logical, see scaleInfReps, and Swish vignette. As this function is primarily for alevin, the default is FALSE

overwrite

logical, whether outfile should overwrite an existing file

...

arguments passed to swish

Value

nothing, files are written out

Details

Note that the default for length correction is FALSE, as opposed to the default in scaleInfReps which is TRUE. The default for numReps here is 20.