import_Vispa2_stats {ISAnalytics} | R Documentation

## Import Vispa2 stats given the aligned association file.

### Description

Imports all the Vispa2 stats files for each pool provided the association file has been aligned with the file system (see `import_association_file`).

### Usage

    import_Vispa2_stats(
      association_file,
      file_prefixes = default_iss_file_prefixes(),
      join_with_af = TRUE,
      pool_col = "concatenatePoolIDSeqRun",
      report_path = default_report_path()
    )

### Arguments

`association_file` | The file system aligned association file (contains columns with absolute paths to the 'iss' folder)
`file_prefixes` | A character vector with known file prefixes to match on file names. NOTE: the elements represent regular expressions. For defaults see default_iss_file_prefixes.
`join_with_af` | Logical, if TRUE the imported stats files will be merged with the association file, if false a single data frame holding only the stats will be returned.
`pool_col` | A single string. What is the name of the pool column used in the Vispa2 run? This will be used as a key to perform a join operation with the stats files `POOL` column.
`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`.

### Value

A data frame

### See Also

Other Import functions: `import_association_file()`, `import_parallel_Vispa2Matrices()`, `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
    )
    stats_files <- import_Vispa2_stats(af,
        join_with_af = FALSE,
        report_path = NULL
    )
    head(stats_files)

[Package ISAnalytics version 1.4.3 Index]