presets: Parameter presets for the 'simulate_alternative_splicing'...

In biomedbigdata/ASimulatoR: Alternative Splicing Simulator

Parameter presets for the simulate_alternative_splicing function

Description

You can pass one of this lists names as parameter preset to simulate_alternative_splicing. This will apply all parameters contained in the corresponding preset. The parameters set by preset can also be overridden using the argument explicitly.

• event_partition: partition exon_supersets in 9 equally sized sets where each set has one event and one set has no event

• experiment_bias: events as in event_partition, but with simulation parameters that correspond to typical experiment biases (illumina sequencing errors, cdna-fragment bias, pcr-bias, adapter-contamination and empirical fragment length distribution)

• event_combination_2: This creates all possible event pairs and give them an equal probability.

• manuscript_use_case: Same preset as used for the use-case in the manuscript. Event probabilities derived from real data.* **This is a computation heavy preset!**

Usage

simulate_alternative_splicing('some_input_dir', 'some_output_dir', preset = 'event_partition')

Format

An object of class list of length 4.

Details

You can check the exact parameters by loading the presets e.g. data(presets); presets$event_partition

Author(s)

Quirin Manz [e-mail]

biomedbigdata/ASimulatoR documentation built on Sept. 6, 2022, 7:55 p.m.