import_parallel_Vispa2Matrices_auto {ISAnalytics}R Documentation

Import integration matrices based on the association file.

Description

[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.

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:

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]