ASimulatoR parameters

Found in file: scripts/ASimulatoR_config.R

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

ncores

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)

multi_events_per_exon

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?

probs_as_freq

T or F

Default:

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.

error_rate

Default: 0.001

In the uniform error model, probability that the sequencer records the wrong nucleotide at any given base.

readlen

Read Length

Default is 76

max_genes

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

seq_depth

Sequencing depth of simulated experiment

num_reps

define, how many groups and samples per group you analyze. Here we create a small experiment with two groups with one sample per group:

as_events

make a list in R with the following set or a subset of the following:

c(‘es’, ‘mes’, ‘ir’, ‘a3’, ‘a5’, ‘afe’, ‘ale’, ‘mee’)

as_combs

Combinations of AS events desired in the simulated dataset.

event_probs

Event probabilities of AS events within the simulated dataset