import_parallel_Vispa2Matrices: Import integration matrices from paths in the association...

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

Import integration matrices from paths in the association file.

Description

The function offers a convenient way of importing multiple integration matrices in an automated or semi-automated way. For more details see the "How to use import functions" vignette: vignette("workflow_start", package = "ISAnalytics")

Usage

import_parallel_Vispa2Matrices(
  association_file,
  quantification_type = c("seqCount", "fragmentEstimate"),
  matrix_type = c("annotated", "not_annotated"),
  workers = 2,
  multi_quant_matrix = TRUE,
  report_path = default_report_path(),
  patterns = NULL,
  matching_opt = matching_options(),
  mode = "AUTO",
  ...
)

Arguments

association_file	Data frame imported via import_association_file (with file system alignment)
quantification_type	A vector of requested quantification_types. Possible choices are quantification_types
matrix_type	A single string representing the type of matrices to be imported. Can only be one in "annotated" or "not_annotated".
workers	A single integer representing the number of parallel workers to use for the import
multi_quant_matrix	If set to TRUE will produce a multi-quantification matrix through comparison_matrix instead of a list.
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.
patterns	A character vector of additional patterns to match on file names. Please note that patterns must be regular expressions. Can be NULL if no patterns need to be matched.
matching_opt	A single value between matching_options
mode	Only AUTO is supported. As of ⁠ISAnalytics 1.8.3⁠, the value INTERACTIVE is officially deprecated.
...	<dynamic-dots> Additional named arguments to pass to comparison_matrix and import_single_Vispa2_matrix

Value

Either a multi-quantification matrix or a list of integration matrices

Required tags

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

• project_id

• vispa_concatenate

See Also

Other Import functions: import_Vispa2_stats(), import_association_file(), import_single_Vispa2Matrix()

Examples

fs_path <- generate_default_folder_structure(type = "correct")
af <- import_association_file(fs_path$af,
    root = fs_path$root,
    report_path = NULL
)
matrices <- import_parallel_Vispa2Matrices(af,
    c("seqCount", "fragmentEstimate"),
    mode = "AUTO", report_path = NULL
)
head(matrices)

calabrialab/ISAnalytics documentation built on Dec. 10, 2024, 10:50 p.m.