generate_default_folder_structure: Generate a default folder structure, following VISPA2...

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Generate a default folder structure, following VISPA2 standards

Description

The function produces a folder structure in the file system at the provided path that respects VISPA2 standards, with package-included data.

Usage

generate_default_folder_structure(
  type = "correct",
  dir = tempdir(),
  af = "default",
  matrices = "default"
)

Arguments

type	One value between "correct", "incorrect" and "both". Tells the function wheter to produce a correct structure or introduce some errors (mainly for testing purposes).
dir	Path to the folder in which the structure will be produced
af	Either "default" for the association file provided as example in the package or a custom association file as a data frame
matrices	Either "default" for integration matrices provided as example in the package or a custom multi-quantification matrix

Value

A named list containing the path to the association file and the path to the top level folder(s) of the structure

Required tags

The function will explicitly check for the presence of these tags:

• project_id

• tag_seq

• vispa_concatenate

See Also

Other Utilities: as_sparse_matrix(), comparison_matrix(), enable_progress_bars(), export_ISA_settings(), generate_Vispa2_launch_AF(), generate_blank_association_file(), import_ISA_settings(), separate_quant_matrices(), transform_columns()

Examples

fs_path <- generate_default_folder_structure(type = "correct")
fs_path

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.