## ----style, echo = FALSE, warning=FALSE, message=FALSE, results = 'asis'---- BiocStyle::markdown() library(knitr) ## ----loadingPackage, warning=FALSE, message=FALSE-------------------------- library(methInheritSim) ## ----caseStudy01, warning=FALSE, message=FALSE, collapse=TRUE-------------- ## Load read DMS dataset (not in this case but normaly) data(samplesForChrSynthetic) ## Print the first three rows of the object head(samplesForChrSynthetic, n = 3) ## ----runSim01, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE----- ## Directory where the files related to the simulation will be saved temp_dir <- "test_runSim" ## Run the simulation runSim(methData = samplesForChrSynthetic, # The dataset use for generate # the synthetic chr. nbSynCHR = 1, # The number of synthetic chromosome nbSimulation = 2, # The number of simulation for each parameter nbBlock = 10, nbCpG = 20, # The number of site in the # synthetic chr is nbBLock * nbCpG nbGeneration = 3, # At least 2 generations must be present vNbSample = c(3, 6), # The number of controls (= number of cases) in # each simulation vpDiff = c(0.9), # Mean proportion of samples with # differentially methylated values vpDiffsd = c(0.1), # Standard deviation associated to vpDiff vDiff = c(0.8), # The shift of the mean of the C/T ratio in # the differentially methylated sites vInheritance = c(0.5), # The proportion of cases that inherit # differentially methylated sites propInherite = 0.3, # The proportion of diffementially methylated # regions that are inherited rateDiff = 0.3, # The mean frequency of the differentially # methylated regions minRate = 0.2, # The minimum rate for differentially # methylated sites propHetero = 0.5, # The reduction of vDiff for the following # generations keepDiff = FALSE, # When FALSE, the differentially methylated # sites are the same in all simulations outputDir = temp_dir, # Directory where files are saved fileID = "S1", runAnalysis = TRUE, nbCores = 1, vSeed = 32) # Fix seed to unable reproductive results # The files generated dir(temp_dir) ## ----removeFiles, warning=FALSE, message=FALSE, collapse=TRUE, echo=FALSE---- if (dir.exists(temp_dir)) { unlink(temp_dir, recursive = TRUE, force = FALSE) } ## ----syntheticChr, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE---- ## The synthetic chromosome syntheticChr <- readRDS("demo_runSim/syntheticChr_S1_1.rds") ## In GRanges format, only Cpg present head(syntheticChr, n=3) ## ----simData, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE------ #### The simulation dataset simData <- readRDS("demo_runSim/simData_S1_1_3_0.9_0.8_0.5_1.rds") #### Information for the first generation F1 head(simData[[1]], n=3) #### Information for the second generation F2 head(simData[[2]], n=3) ## ----stateDiff, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE---- #### The DMS state information stateDiff <- readRDS("demo_runSim/stateDiff_S1_1_3_0.9_0.8_0.5_1.rds") #### In stateDiff, the position of DMS is indicated by 1 #### in stateInherite, the position of inherited DMS is indicated by 1 head(stateDiff) ## ----methylGR, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE----- #### The raw methylation data in GRanges methylGR <- readRDS("demo_runSim/methylGR_S1_1_3_0.9_0.8_0.5_1.rds") #### The third sample of the first generation head(methylGR[[1]][[3]], n = 3) #### The fourth sample of the third generation head(methylGR[[3]][[4]], n = 3) ## ----treatment, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE---- #### The information about controls and cases treatment <- readRDS("demo_runSim/treatment_S1_1_3.rds") #### 0 = control, 1 = case, length = number of samples head(treatment) ## ----methylObj, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE---- ## The raw methylation data methylObj <- readRDS("demo_runSim/methylObj_S1_1_3_0.9_0.8_0.5_1.rds") #### The third sample of the first generation head(methylObj[[1]][[3]], n = 3) #### The fourth sample of the third generation head(methylObj[[3]][[4]], n = 3) ## ----meth, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE--------- #### The methylation events present in multiple samples meth <- readRDS("demo_runSim/meth_S1_1_3_0.9_0.8_0.5_1.rds") #### Information for all samples in the first generation head(meth[[1]], n = 3) ## ----methDiff, warning=FALSE, message=FALSE, collapse=TRUE, cache=TRUE----- #### The differential methylation statistics methDiff <- readRDS("demo_runSim/methDiff_S1_1_3_0.9_0.8_0.5_1.rds") #### Information for the first generation head(methDiff[[1]], n = 3)