import_parallel_Vispa2Matrices_auto {ISAnalytics} | R Documentation

## Import integration matrices based on the association file.

### Description

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

### 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
`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`

### 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

### Automatic version

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

### 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

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

Other Import functions: `import_Vispa2_stats()`, `import_association_file()`, `import_parallel_Vispa2Matrices_interactive()`, `import_single_Vispa2Matrix()`

### Examples

    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)

[Package ISAnalytics version 1.2.1 Index]