import_parallel_Vispa2Matrices {ISAnalytics} | R Documentation

## 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("import_functions_howto", package = "ISAnalytics")`

### Usage

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

### Arguments

`association_file` | Data frame imported via import_association_file (with file system alignment) or a string containing the path to the association file on disk.
`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, a file or NULL if no report should be produced. Defaults to `{user_home}/ISAnalytics_reports`.
`patterns` | Relevant only if argument `mode` is set to `AUTO`. 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` | Relevant only if argument `mode` is set to `AUTO`. A single value between matching_options
`mode` | A single value between `AUTO` and `INTERACTIVE`. If INTERACTIVE, the function will ask for input from the user on console, otherwise the process is fully automated (with limitations, see vignette).
`...` | <`dynamic-dots`> Additional named arguments to pass to `ìmport_association_file` and `comparison_matrix`

### Value

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

### See Also

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

### Examples

    fs_path <- system.file("extdata", "fs.zip", package = "ISAnalytics")
    fs <- unzip_file_system(fs_path, "fs")
    af_path <- system.file("extdata", "asso.file.tsv.gz",
        package = "ISAnalytics"
    )
    af <- import_association_file(af_path,
        root = fs,
        import_iss = FALSE,
        report_path = NULL
    )
    matrices <- import_parallel_Vispa2Matrices(af,
        c("seqCount", "fragmentEstimate"),
        mode = "AUTO", report_path = NULL
    )
    head(matrices)

[Package ISAnalytics version 1.4.3 Index]