omicSettings {MOSim} | R Documentation

## Retrieves the settings used in a simulation

### Description

Retrieves the settings used in a simulation

### Usage

    omicSettings(simulation, omics = NULL, association = FALSE,
      reverse = FALSE, only.linked = FALSE, prefix = FALSE,
      include.lagged = TRUE)

### Arguments

`simulation` | A MOSimulation object.
`omics` | List of omics to retrieve the settings.
`association` | A boolean indicating if the association must also be returned for the regulators.
`reverse` | A boolean, swap the column order in the association list in case we want to use the output directly and the program requires a different ordering.
`only.linked` | Return only the interactions that have an effect.
`prefix` | Logical indicating if the name of the omic should prefix the name of the regulator.
`include.lagged` | Logical indicating if interactions with transitory profile and different minimum/maximum time point between gene and regulator should be included or not.

### Value

A list containing a data frame with the settings used to simulate each of the indicated omics. If association is TRUE, it will be a list with 3 keys: 'associations', 'settings' and 'regulators', with the first two keys being a list containing the information for the selected omics and the last one a global data frame giving the merged information.

### Examples

    omic_list <- c("RNA-seq", "miRNA-seq")
    multi_simulation <- mosim(omics = omic_list)

    # This will be a data frame with RNA-seq settings (DE flag, profiles)
    rnaseq_settings <- omicSettings(multi_simulation, "RNA-seq")

    # This will be a list containing all the simulated omics (RNA-seq
    # and DNase-seq in this case)
    all_settings <- omicSettings(multi_simulation)

[Package MOSim version 1.8.0 Index]