extraction: Extraction of object from file or object
In MathurinD/STASNet: Fit and Simulate Model from Perturbation Data

Description Usage Arguments Details Value See Also

Extraction of object from file or object

'extractStructure' detects the format of the structure file and extract the structure of the network. It expects a matrix with 2 or 3 columns (adjacency list) or a square matrix (adjacency matrix)

'extractBasalActivity' detects if the a list of names or a file perform the extraction if necessary. It expects a vector or an object convertible to a vector.

'extractMIDAS' detects if the argument is a MIDAS dataset or the name of a file containing such dataset. It expects a matrix in MIDAS format (See Details).

extractStructure(to_detect, names = "", adj = FALSE)

extractBasalActivity(to_detect)

extractMIDAS(to_detect)

`to_detect`	An object to check or a string. A string is interpreted as a path to a file containing a matrix compatible with the target object.
`adj`	Boolean, whether a 2 or 3 columns matrix in to_detect should be interpreted as an adjacency matrix
`name`	Name for the structure. Extracted automatically from the file name if used.

A MIDAS format matrix is a matrix with specific column names:

One column 'ID:type' containing the type of experiment of each row:
- 'c' or 'control' for control experiment with no treatment
- 'blank' for blank experiment with no treatment
- 't' for experiment with a treatment
At least one column 'TR:STIMULATION' or 'TR:INHIBITIONi' containing 0 or 1 whether the perturbation is applied for the experiment in each row
One column 'DA:all' or the relevant number of columns 'DA:PERTURBATION' containing the time of the perturbation (Not used in STASNet)
At least one column with column name 'DV:READOUT' containing the measured values for each readout