import_parallel_Vispa2Matrices_auto: 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 Usage Arguments Details Value Automatic version Interactive version See Also Examples

\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.

import_parallel_Vispa2Matrices_auto(
  association_file,
  quantification_type,
  matrix_type = "annotated",
  workers = 2,
  multi_quant_matrix = TRUE,
  export_report_path = NULL,
  patterns = NULL,
  matching_opt = matching_options(),
  ...
)

`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
`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 needs to be matched.
`matching_opt`	A single value between `matching_options`
`...`	<`dynamic-dots`> Additional named arguments to pass to `ìmport_association_file` and `comparison_matrix`

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")

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

The automatic version of import_parallel_Vispa2Matrices doesn't interact with the user directly, for this reason options in this modality are more limited compared to the interactive version. In automatic version you can't:

Choose single projects or pools: to have a selection import the association file first and filter it according to your needs before calling the function (more details on this in the vignette)
Choose duplicates: if, after filtering by the specified patterns, duplicates are found they are automatically ignored

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.

matching_options, https://stringr.tidyverse.org/articles/regular-expressions.html

Other Import functions: import_association_file(), import_parallel_Vispa2Matrices_interactive(), import_single_Vispa2Matrix()

op <- options("ISAnalytics.widgets" = FALSE)
path <- system.file("extdata", "ex_association_file.tsv",
    package = "ISAnalytics"
)
root_pth <- system.file("extdata", "fs.zip", package = "ISAnalytics")
root <- unzip_file_system(root_pth, "fs")
matrices <- import_parallel_Vispa2Matrices_auto(
    association_file = path,
    quantification_type = c("fragmentEstimate", "seqCount"),
    patterns = NULL, matching_opt = "ANY",
    root = root,
    dates_format = "dmy",
    workers = 2
)
options(op)