generate_Vispa2_launch_AF: Creates a reduced association file for a VISPA2 run, given...

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

Creates a reduced association file for a VISPA2 run, given project and pool

Description

The function selects the appropriate columns and prepares a file for the launch of VISPA2 pipeline for each project/pool pair specified.

Usage

generate_Vispa2_launch_AF(association_file, project, pool, path)

Arguments

association_file	The imported association file (via import_association_file())
project	A vector of characters containing project names
pool	A vector of characters containing pool names
path	A single string representing the path to the folder where files should be written. If the folder doesn't exist it will be created.

Details

Note: the function is vectorized, meaning you can specify more than one project and more than one pool as vectors of characters, but you must ensure that:

• Both project and pool vectors have the same length

• You correclty type names in corresponding positions, for example c("PJ01", "PJ01") - c("POOL01", "POOL02"). If you type a pool in the position of a corresponding project that doesn't match no file will be produced since that pool doesn't exist in the corresponding project.

Value

NULL

Required tags

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

• cell_marker

• fusion_id

• pcr_repl_id

• pool_id

• project_id

• subject

• tag_id

• tissue

• tp_days

• vector_id

The names of the pools in the pool argument is checked against the column corresponding to the pool_id tag.

See Also

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

Examples

temp <- tempdir()
data("association_file", package = "ISAnalytics")
generate_Vispa2_launch_AF(association_file, "PJ01", "POOL01", temp)

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