## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    dpi = 72,
    fig.width = 5,
    fig.height = 4
)

## ----load_package, include = FALSE--------------------------------------------
# Load the package
library(STADyUM)

## ----create_simpol, fig.width=7,fig.height=5,out.width="70%",out.height="50%"----
simpol <- simulatePolymerase(k=50, ksd=25, kMin=17, kMax=200, geneLen=1950,
alpha=2, beta=0.5, zeta=2000, zetaSd=1000, zetaMin=1500, zetaMax=2500,
cellNum=100, polSize=33, addSpace=17, time=39, timesToRecord=NULL)

show(simpol)

readCounts <- readCounts(simpol)

plotCombinedCells(simpol, file="combinedCellsLollipopPlot.png")

## ----estimate_simulated_rates, fig.width=7, fig.height=5, out.width="75%"-----
simRates <- estimateTranscriptionRates(simpol, name="simRatesb0.5k50",
stericHindrance=TRUE)

show(simRates)

## ----simulated_lrts, fig.width=7, fig.height=5, out.width="75%"---------------

simpol2 <- simulatePolymerase(k=100, ksd=25, kMin=75, kMax=200, geneLen=1950,
alpha=2, beta=10, zeta=2000, zetaSd=1000, zetaMin=1500, zetaMax=2500,
cellNum=100, polSize=33, addSpace=17, time=30, timesToRecord=NULL)

simRates2 <- estimateTranscriptionRates(simpol2, name="simRatesb10k100",
stericHindrance=TRUE)

simLRT <- likelihoodRatioTest(simRates, simRates2)

plotPauseSiteContourMapTwoConditions(simLRT, file="simPauseSitesContourMap.png",
                                      width=7, height=5, dpi=150)
BetaViolinPlot(simLRT, file="simBetaViolinPlot.png", width=5, height=4.5, dpi=150)


## ----session_info-------------------------------------------------------------
sessionInfo()