miniSwish: Helper function for distributing Swish on a subset of data

In mikelove/fishpond: Fishpond: downstream methods and tools for expression data

Helper function for distributing Swish on a subset of data

Description

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.

Usage

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

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.

Value

nothing, files are written out

mikelove/fishpond documentation built on Aug. 29, 2023, 2:45 p.m.