Nothing
## ----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)
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