import_Vispa2_stats: Import Vispa2 stats given the aligned association file.

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

Import Vispa2 stats given the aligned association file.

Description

Imports all the Vispa2 stats files for each pool provided the association file has been aligned with the file system (see import_association_file).

Usage

import_Vispa2_stats(
  association_file,
  file_prefixes = default_iss_file_prefixes(),
  join_with_af = TRUE,
  pool_col = "concatenatePoolIDSeqRun",
  report_path = default_report_path()
)

Arguments

association_file	The file system aligned association file (contains columns with absolute paths to the 'iss' folder)
file_prefixes	A character vector with known file prefixes to match on file names. NOTE: the elements represent regular expressions. For defaults see default_iss_file_prefixes.
join_with_af	Logical, if TRUE the imported stats files will be merged with the association file, if FALSE a single data frame holding only the stats will be returned.
pool_col	A single string. What is the name of the pool column used in the Vispa2 run? This will be used as a key to perform a join operation with the stats files POOL column.
report_path	The path where the report file should be saved. Can be a folder or NULL if no report should be produced. Defaults to {user_home}/ISAnalytics_reports.

Value

A data frame

Required tags

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

• project_id

• tag_seq

• vispa_concatenate

• pcr_repl_id

See Also

Other Import functions: import_association_file(), import_parallel_Vispa2Matrices(), import_single_Vispa2Matrix()

Examples

fs_path <- generate_default_folder_structure(type = "correct")
af <- import_association_file(fs_path$af,
    root = fs_path$root,
    import_iss = FALSE,
    report_path = NULL
)
stats_files <- import_Vispa2_stats(af,
    join_with_af = FALSE,
    report_path = NULL
)
head(stats_files)

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