writeresidencyG_folder Function

Generate G state residency probabilities for GRSM models.

Syntax

write_residency_G_folder(; kwargs...)

Arguments

Model Parameters

• G::Int = 2: Number of gene states
• R::Int = 0: Number of pre-RNA steps
• S::Int = 0: Number of splice sites
• insertstep::Int = 1: Reporter insertion step
• transitions::Tuple = (): State transitions
• rates::Vector{Float64}: Model rates
• nalleles::Int = 1: Number of alleles

Simulation Parameters

• ntraces::Int = 1000: Number of traces
• tspan::Tuple{Float64, Float64} = (0., 1000.): Time span for traces
• dt::Float64 = 1.0: Time step
• burnin::Float64 = 0.0: Burn-in time
• sampletime::Float64 = 1.0: Sampling interval

Output Parameters

• outfolder::String = "residency": Output folder
• label::String = "": Output file label
• write::Bool = true: Write residency data to file
• returnresidency::Bool = false: Return residency data

Returns

• residency: Array of residency probabilities for each G state

Examples

# Generate residency for a simple G model
write_residency_G_folder(
    G = 2,
    R = 0,
    rates = [0.1, 0.2],  # G1->G2, G2->G1
    ntraces = 1000,
    tspan = (0., 1000.),
    dt = 1.0
)

# Generate residency for a GR model
write_residency_G_folder(
    G = 2,
    R = 3,
    S = 2,
    insertstep = 1,
    rates = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6],
    ntraces = 5000,
    tspan = (0., 2000.),
    dt = 0.5,
    burnin = 100.0,
    sampletime = 5.0
)

Notes

1. Residency Calculation

   • Traces are generated using Gillespie algorithm
   • Residency is calculated as fraction of time in each G state
   • Results are averaged over all traces

2. Rate Order

   • G transitions
   • R transitions
   • S transitions
   • Decay