Dwell Time Analysis

This example demonstrates how to analyze dwell time distributions from live cell imaging data.

Setup

First, let's set up our project directory and load the package:

using StochasticGene

# Create project directory
rna_setup("dwell_example")
cd("dwell_example")

Data Preparation

Place your dwell time data in the data/ directory. The data should be in a format compatible with the package (see Data Types for details).

Model Definition

We'll fit a model with:

• 2 gene states (G=2)
• No pre-RNA steps (R=0)
• Simple transitions between states

# Define model parameters
G = 2  # Number of gene states
R = 0  # Number of pre-RNA steps
transitions = ([1,2], [2,1])  # Gene state transitions

Fitting the Model

Now we can fit the model to our dwell time data:

# Fit the model
fits, stats, measures, data, model, options = fit(
    G = G,
    R = R,
    transitions = transitions,
    datatype = "dwell",
    datapath = "data/",
    gene = "PP7",
    datacond = "CONTROL"
)

Analyzing Results

Let's examine the fitting results:

# Print basic statistics
println(stats)

# Plot the results
using Plots
plot(fits)

# Fit writes rates, measures, and parameter statistics under `resultfolder`.

Model Interpretation

The fitted model provides:

• Gene state transition rates
• Dwell time distributions
• Model likelihood and fit statistics

Advanced Analysis

ON/OFF Histograms

# Generate ON/OFF histograms
write_ONOFFhistograms(fits, "results/")

State Residency

# Calculate state residency probabilities
write_residency_G_folder("results/my-run")

Burst Analysis

# For burst summaries, run fits with `burst=true` and inspect the burst output
# files written by `fit`.

Next Steps

• Try fitting models with multiple states
• Experiment with different transition configurations
• Compare results across different genes

For more advanced examples, see:

• Coupled States
• Multiple Conditions
• Hierarchical Models