R: Import integration matrices from paths in the association...

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

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)