create_container_command: Creation of the docker command

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

Creation of the docker command

Description

Creation of the docker command

Usage

create_container_command(
  in_dir,
  out_dir,
  container = c("docker", "apptainer"),
  apptainer_container_path = NULL,
  method = c("create_sig", "impute_cell_fractions"),
  verbose = FALSE,
  ...
)

Arguments

in_dir	The folder in which the input files can be found (or are created in). Default is a temporary directory.
out_dir	The directory in which the output files are saved. Default is a temporary directory.
container	The container to use. Possibilities are 'docker' and 'apptainer'
apptainer_container_path	The path where the apptainer container is stored (optional)
method	Which docker command should be be created. For signature matrix creation use "create_sig", for cell type deconvolution use "impute_cell_fractions".
verbose	Whether to produce an output on the console.
...	The additional parameters for the command.

Value

A valid docker command to be run.

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.