import_association_file {ISAnalytics} | R Documentation |
Imports the association file and immediately performs a check on
the file system starting from the root to assess the alignment between the
two.
import_association_file( path, root = NULL, tp_padding = 4, dates_format = "ymd", separator = "\t", filter_for = NULL, import_iss = FALSE, convert_tp = TRUE, report_path = default_report_path(), ... )
path |
The path on disk to the association file. |
root |
The path on disk of the root folder of Vispa2 output or NULL. See details. |
tp_padding |
Timepoint padding, indicates the number of digits of the "TimePoint" column once imported. Fills the content with 0s up to the length specified (ex: 1 becomes 0001 with a tp_padding of 4) |
dates_format |
A single string indicating how dates should be parsed.
Must be a value in: |
separator |
The column separator used in the file |
filter_for |
A named list where names represent column names that
must be filtered. For example: |
import_iss |
Import Vispa2 stats and merge them with the association file? |
convert_tp |
Should be time points be converted into months and years? |
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 |
... |
Additional arguments to pass to
|
If the root
argument is set to NULL
no file system alignment is
performed. This allows to import the basic file but it won't be
possible to perfom automated matrix and stats import.
For more details see the "How to use import functions" vignette:
vignette("import_functions_howto", package = "ISAnalytics")
The data frame holding metadata
Other Import functions:
import_Vispa2_stats()
,
import_parallel_Vispa2Matrices()
,
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, report_path = NULL) head(af)