salmon: Run Salmon

In hugheylab/seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data

Run Salmon

Description

This function calls salmon using system2(). To run in parallel, register a parallel backend, e.g., using doParallel::registerDoParallel().

Usage

salmon(
  filepaths,
  samples,
  indexDir,
  outputDir = "salmon_output",
  cmd = "salmon",
  args = c("-l A -q --seqBias --gcBias --no-version-check -p",
    foreach::getDoParWorkers()),
  compress = TRUE
)

Arguments

filepaths	Paths to fastq files. For single-end reads, each element should be a single filepath. For paired-end reads, each element should be two filepaths separated by ";".
samples	Corresponding sample names for fastq files.
indexDir	Directory that contains salmon index.
outputDir	Directory in which to store output. Will be created if it doesn't exist.
cmd	Name or path of the command-line interface.
args	Additional arguments to pass to the command-line interface.
compress	Logical indicating whether to gzip the quantification file (quant.sf) from salmon. Does not affect downstream analysis.

Value

A vector of exit codes, invisibly.

See Also

seeker(), getSalmonMetadata()

hugheylab/seeker documentation built on Aug. 28, 2024, 8:20 a.m.