R6 class representing ProlfquApp configuration

Description

R6 class representing ProlfquApp configuration

R6 class representing ProlfquApp configuration

Public fields

processing_options
ProcessingOption R6 class
project_spec
Project Spec R6 class
software
name of input software
prefix
either QC or DEA
zipdir_name
results should go to zipdir_name
flat_outdir
when TRUE, write results directly into ‘path’ with no dated zipdir subdir (default FALSE keeps the dated layout)
path
path to working directory
group
group prefix
ext_reader
external reader configuration

Methods

Public methods

Method new()

Initialize ProlfquAppConfig with processing options, project spec, and external reader

Usage 
ProlfquAppConfig\$new(
  processing_options,
  project_spec,
  ext_reader,
  zipdir_name = ".",
  path = ".",
  software = "DIANN",
  prefix = "DEA",
  flat_outdir = FALSE
)
Arguments
processing_options
instance of ProcessingOptions
project_spec
instance of ProjectSpec
ext_reader
instance of ExternalReader
zipdir_name
where to store results
path
working directory path
software
name of input software
prefix
either QC or DEA
flat_outdir
write results directly into ‘path’ without a dated subdir (default FALSE)

Method set_zipdir_name()

Set zip directory name based on project information and date

Usage 
ProlfquAppConfig\$set_zipdir_name()
Returns

the generated zip directory name

Method get_zipdir()

Get the full path to the zip directory

When ‘flat_outdir’ is TRUE the dated zipdir subdir is skipped and results are written directly into ‘path’.

Usage 
ProlfquAppConfig\$get_zipdir()
Returns

full path to zip directory

Method get_result_dir()

Get the results directory path

Usage 
ProlfquAppConfig\$get_result_dir()
Returns

path to results directory

Method get_input_dir()

Get the input directory path

Usage 
ProlfquAppConfig\$get_input_dir()
Returns

path to input directory

Method as_list()

Convert R6 object to list

Usage 
ProlfquAppConfig\$as_list()
Returns

list representation of the R6 object

Method clone()

The objects of this class are cloneable with this method.

Usage 
ProlfquAppConfig\$clone(deep = FALSE)
Arguments
deep
Whether to make a deep clone.

See Also

Other ProlfquAppConfig: ExternalReader, ProcessingOptions, ProjectSpec, make_DEA_config_R6(), set_list_to_R6()

Examples

library("prolfquapp")



r6obj_config <- ProlfquAppConfig$new(
  ProcessingOptions$new(),
  ProjectSpec$new(),
  ExternalReader$new()
)
xx <- prolfqua::R6_extract_values(r6obj_config)
yaml::write_yaml(xx, file = file.path(tempdir(), "test.yaml"))
config <- yaml::read_yaml(file = file.path(tempdir(), "test.yaml"))

r6obj_config$set_zipdir_name()
[1] "DEA_20260729_vsn"
r6obj_config$get_zipdir()
[1] "./DEA_20260729_vsn"
r6obj_config$get_result_dir()
[1] "./DEA_20260729_vsn/Results_WU_"
r6obj_config$get_input_dir()
[1] "./DEA_20260729_vsn/Inputs_WU_"