import_Vispa2_stats {ISAnalytics}R Documentation

Import Vispa2 stats given the aligned association file.

Description

[Experimental] 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",
  export_widget_path = NULL
)

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.

export_widget_path

Either NULL or the path on disk where the widget report should be saved.

Value

A data frame

See Also

Other Import functions: import_association_file(), import_parallel_Vispa2Matrices_auto(), 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")
association_file <- import_association_file(path, root, dates_format = "dmy")
af_with_stats <- import_Vispa2_stats(association_file)
options(op)

[Package ISAnalytics version 1.2.1 Index]