import_parallel_Vispa2Matrices_interactive {ISAnalytics}R Documentation

Import integration matrices based on the association file.

Description

[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)

[Package ISAnalytics version 1.0.11 Index]