omicSettings: Retrieves the settings used in a simulation

In Neurergus/MOSim: Multi-Omics Simulation (MOSim)

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)

Neurergus/MOSim documentation built on Feb. 23, 2024, 8:29 a.m.