ASimulatoR parameters

Found in file: scripts/ASimulatoR_config.R

Parameters are also explained in the following git github/biomedbigdata/ASimulatoR

Number of cores used by ASimulatoR
Within dicast, the max number of cores supplied to Snakemake, is as much is used within DICAST’s pipeline. ( See Snakemake parameters)
T or F
Should 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?
T or F
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: 0.001
In the uniform error model, probability that the sequencer records the wrong nucleotide at any given base.
Read Length
Default 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