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Run Terminus on Salmon output from R

Source: R/terminus.R
run_terminus.Rd

run_terminus() builds the consensus groups of Terminus for a set of samples without leaving R: it runs terminus group on every Salmon output directory, then terminus collapse on all of them, and returns the groups read by read_terminus_groups(), ready for add_uncertainty(groups = ). Terminus is installed from Bioconda into a conda environment managed by condathis the first time it is needed.

Usage

run_terminus(
  paths,
  output_dir,
  consensus_thresh = 0.5,
  min_spread = 0.1,
  threads = 4L,
  workers = 1L,
  keep_logs = FALSE,
  env_name = "terminus-env",
  verbose = "output"
)

Arguments

paths

Salmon output directories (or paths to their quant.sf).

output_dir

Folder for the Terminus output; one subfolder per sample holds groups.txt and, after the consensus, clusters.txt and the collapsed quantification.

consensus_thresh

Share of samples in which two transcripts must be grouped for the consensus to group them (--consensus-thresh).

min_spread

Minimum spread of a transcript for its edges to be collapse candidates (--min-spread).

threads

Threads for writing the collapsed quantifications.

workers

Number of samples grouped at the same time (in parallel processes on Unix-like systems). Each one needs several gigabytes of memory for a human transcriptome.

keep_logs

Logical, keep the logs of terminus group.

env_name

Name of the conda environment with Terminus.

verbose

Passed to condathis::run().

Value

The consensus groups, as returned by read_terminus_groups(), with the output folder in the output_dir attribute.

Details

Every directory needs inferential replicates (--numGibbsSamples or --numBootstraps) and equivalence classes with their weights (--dumpEq --dumpEqWeights); salmon_quant() writes both. Without the weights Terminus stops with an unhelpful error, so the directories are checked first. Terminus names the folder of each sample after the basename of its Salmon directory, which must therefore be unique.

terminus group writes a log of several gigabytes per human sample (delta.log) that collapse does not use; it is deleted as soon as each sample is grouped, and the other logs after the consensus, unless keep_logs = TRUE.

See also

read_terminus_groups(), add_uncertainty(), salmon_quant()

Examples

if (FALSE) { # \dontrun{
groups <- run_terminus(quant_dirs, output_dir = "terminus")
iso <- add_uncertainty(iso, paths = quant_dirs, groups = groups)
tx_uncertainty(iso)
} # }