import_parallel_Vispa2Matrices {ISAnalytics} | R Documentation |
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")
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"), ... )
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 |
patterns |
Relevant only if argument |
matching_opt |
Relevant only if argument |
mode |
A single value between |
... |
< |
Either a multi-quantification matrix or a list of integration matrices
Other Import functions:
import_Vispa2_stats()
,
import_association_file()
,
import_single_Vispa2Matrix()
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)