salmon {seeker}

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()