write_traces Function

Generate model-predicted intensity traces for GRSM models.

Syntax

write_traces(; 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

Trace Parameters

• ntraces::Int = 100: Number of traces to generate
• tspan::Tuple{Float64, Float64} = (0., 100.): Time span for traces
• dt::Float64 = 1.0: Time step
• noise::Vector{Float64} = Float64[]: Observation noise parameters
• probfn::Function = prob_Gaussian: Observation probability function

Output Parameters

• outfolder::String = "traces": Output folder
• label::String = "": Output file label
• write::Bool = true: Write traces to file
• returntraces::Bool = false: Return traces array

Returns

• traces: Array of generated traces (if returntraces = true)

Examples

# Generate traces for a simple G model
write_traces(
    G = 2,
    R = 0,
    rates = [0.1, 0.2],  # G1->G2, G2->G1
    ntraces = 100,
    tspan = (0., 100.),
    dt = 1.0
)

# Generate traces for a GR model
write_traces(
    G = 2,
    R = 3,
    S = 2,
    insertstep = 1,
    rates = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6],
    ntraces = 50,
    tspan = (0., 200.),
    dt = 0.5
)

Notes

1. Rate Order

   • G transitions
   • R transitions
   • S transitions
   • Decay
   • Noise parameters

2. Trace Generation

   • Traces are generated using Gillespie algorithm
   • Noise is added according to specified probfn
   • Output format: time, intensity, G state, R state, S state