import_parallel_Vispa2Matrices_interactive: Import integration matrices based on the association file.

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

Description

\lifecycle

maturing These functions are designed to import the appropriate integration matrix files given the association file and the root folder of the file system where Vispa2 matrices are generated.

Usage

import_parallel_Vispa2Matrices_interactive(
  association_file,
  quantification_type,
  matrix_type = "annotated",
  workers = 2,
  multi_quant_matrix = TRUE,
  export_report_path = NULL,
  ...
)

Arguments

association_file	A single string containing the path to the association file on disk, or a data frame resulting from a previous call to import_association_file
quantification_type	A vector of requested quantification_types. Must be one in 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 (data frame) through comparison_matrix instead of a list.
export_report_path	A path on disk to save produced import report or NULL if the user doesn't wish to save the html file
...	<dynamic-dots> Additional named arguments to pass to ìmport_association_file and comparison_matrix

Details

Import family functions are designed to work in combination with Vispa2, for more details on this take a look here: VISPA2: A Scalable Pipeline for High-Throughput Identification and Annotation of Vector Integration Sites.
For more details on how to properly use these functions, refer to the vignette - vignette("how_to_import_functions")

Value

A named list of data frames containing data from all imported integration matrices, divided by quantification type or a multi-quantification matrix

Interactive version

The interactive version of import_parallel_Vispa2Matrices asks user for input and allows a more detailed choice of projects to import, pools to import and, if necessary, duplicate files. During the execution, a series of reports is shown in html format.

See Also

comparison_matrix, import_association_file

Other Import functions: import_association_file(), import_parallel_Vispa2Matrices_auto(), import_single_Vispa2Matrix()

Examples

## Not run: 
# Can't run because it's interactive and requires user input
matrices <- import_parallel_Vispa2Matrices_interactive(
    association_file,
    quantification_type,
    matrix_type = "annotated",
    workers = 2,
    multi_quant_matrix = FALSE,
    export_report_path = NULL,
)

## End(Not run)

ISAnalytics documentation built on April 9, 2021, 6:01 p.m.