Found in file: scripts/ASimulatoR_config.R
Parameters are also explained in the following git github/biomedbigdata/ASimulatoR
- Number of cores used by ASimulatoRWithin dicast, the max number of cores supplied to Snakemake, is as much is used within DICAST’s pipeline. ( See Snakemake parameters)
FShould each exon be treated as a target for only one Alternative Splicing event or would you like to see events like Multiple Exon Skipping events, Alternative Last/First Exon + Exon Skipping events?
F: if probs_as_freq was FALSE, a random number would be drawn for each event-superset combination and only if it was smaller than 1/9 the AS event would be created
T: The exon supersets are partitioned corresponding to the event_prob parameter.
- Default: 0.001In the uniform error model, probability that the sequencer records the wrong nucleotide at any given base.
- Read LengthDefault is 76
- define the number of genes you want to work with. If you want all exons, do not specify this parameter or set it to NULL
- Sequencing depth of simulated experiment
- define, how many groups and samples per group you analyze. Here we create a small experiment with two groups with one sample per group:
- make a list in R with the following set or a subset of the following:c(‘es’, ‘mes’, ‘ir’, ‘a3’, ‘a5’, ‘afe’, ‘ale’, ‘mee’)
- Combinations of AS events desired in the simulated dataset.
- Event probabilities of AS events within the simulated dataset