import_parallel_Vispa2Matrices_auto: Import integration matrices based on the association file.

Description Usage Arguments Details Value Automatic version Interactive version See Also Examples

View source: R/import-functions.R

Description

\lifecycle

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

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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_association_file(), import_parallel_Vispa2Matrices_interactive(), import_single_Vispa2Matrix()

Examples

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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)

ISAnalytics documentation built on April 9, 2021, 6:01 p.m.