## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  fig.width = 8,
  collapse = TRUE,
  comment = "#>"
)

## ----style, echo = FALSE, results = 'asis'------------------------------------
BiocStyle::markdown()

## ---- setup, message=F--------------------------------------------------------
library(knitr)

## ----Information on CpGs in MEAT, eval=FALSE----------------------------------
#  data("CpGs_in_MEAT",envir = environment())

## ----Information on CpGs in MEAT2.0, eval=FALSE-------------------------------
#  data("CpGs_in_MEAT2.0",envir = environment())

## ----MEAT package installation, eval=FALSE------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("MEAT")

## ----MEAT package installation loading, message=FALSE, warning=FALSE----------
library(MEAT)

## ----Methylation matrix presentation------------------------------------------
data("GSE121961", envir = environment())

## ----Methylation matrix presentation table, echo = FALSE----------------------
kable(head(GSE121961),
             caption = "Top rows of the GSE121961 matrix before cleaning and calibration.")

## ----Phenotype table presentation---------------------------------------------
data("GSE121961_pheno", envir = environment())

## ----Phenotype table presentation table, echo = FALSE-------------------------
kable(GSE121961_pheno,
             caption = "Phenotypes corresponding to GSE121961.")

## ----Data formatting, message=FALSE, warning=FALSE----------------------------
library(SummarizedExperiment)
GSE121961_SE <- SummarizedExperiment(assays=list(beta=GSE121961),
colData=GSE121961_pheno)
GSE121961_SE

## ----Data cleaning, message=FALSE, warning=FALSE------------------------------
GSE121961_SE_clean <- clean_beta(SE = GSE121961_SE,
                                 version = "MEAT2.0")

## ----Data cleaning table, echo = FALSE----------------------------------------
kable(head(assays(GSE121961_SE_clean)$beta),
             caption = "Top rows of the GSE121961 beta matrix after cleaning.")

## ----Data calibration, message=FALSE, warning=FALSE---------------------------
GSE121961_SE_calibrated <- BMIQcalibration(SE = GSE121961_SE_clean,
                                           version = "MEAT2.0")

## ----Data calibration table, echo=FALSE---------------------------------------
kable(head(assays(GSE121961_SE_calibrated)$beta),
             caption = "Top rows of the GSE121961 beta matrix after cleaning and calibration.")

## ----DNA methylation profile distribution before and after calibration, message=FALSE, warning=FALSE----
data("gold.mean.MEAT2.0", envir = environment())
GSE121961_SE_clean_with_gold_mean <- cbind(assays(GSE121961_SE_clean)$beta,
                                           gold.mean.MEAT2.0$gold.mean) # add the gold mean
GSE121961_SE_calibrated_with_gold_mean <- cbind(assays(GSE121961_SE_calibrated)$beta,
                                                gold.mean.MEAT2.0$gold.mean) # add the gold mean
groups <- c(rep("GSE121961",
                ncol(GSE121961_SE_clean)), "Gold mean")

library(minfi)
par(mfrow = c(2, 1))
densityPlot(GSE121961_SE_clean_with_gold_mean,
  sampGroups = groups,
  main = "Before calibration",
  legend = FALSE
)
densityPlot(GSE121961_SE_calibrated_with_gold_mean,
  sampGroups = groups,
  main = "After calibration"
)

## ----Epigenetic age estimation with phenotypes, message=FALSE, warning=FALSE----
GSE121961_SE_epiage <- epiage_estimation(SE = GSE121961_SE_calibrated,
                                         age_col_name = "Age",
                                         version = "MEAT2.0")

## ----Epigenetic age estimation with phenotypes table, echo=FALSE--------------
kable(colData(GSE121961_SE_epiage),
             caption = "Phenotypes corresponding to GSE121961 with AAdiff for each sample.")

## ----session info-------------------------------------------------------------
sessionInfo()

