import_parallel_Vispa2Matrices_auto {ISAnalytics} | R Documentation |
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.
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(), ... )
association_file |
A single string containing the path to the
association file on disk, or a data frame resulting from a previous call to
|
quantification_type |
A vector of requested quantification_types. Must
be one in |
matrix_type |
A single string representing the type of matrices to
be imported. Can only be one in |
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 |
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 |
... |
< |
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")
A named list of data frames containing data from all imported integration matrices, divided by quantification type or a multi-quantification matrix
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:
Choose single projects or pools: to have a selection import the association file first and filter it according to your needs before calling the function (more details on this in the vignette)
Choose duplicates: if, after filtering by the specified patterns, duplicates are found they are automatically ignored
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.
matching_options
,
https://stringr.tidyverse.org/articles/regular-expressions.html
Other Import functions:
import_association_file()
,
import_parallel_Vispa2Matrices_interactive()
,
import_single_Vispa2Matrix()
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)