Source: TBA

Introduction

baseDir=getwd()
dataDir=paste(baseDir,"/him_chart_idats/CHART_idats",sep="")

suppressPackageStartupMessages({
  library("missMethyl")
  library("limma")
  library("minfi")
  library("IlluminaHumanMethylation450kanno.ilmn12.hg19")
  library("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")
  library("ruv")
  library("RColorBrewer")
  library("matrixStats")
  library("gplots")
  library("FlowSorted.Blood.450k")
  library("reshape2")
  library("ggplot2")
  library("DMRcate")
  library("FlowSorted.Blood.EPIC")
  library("mitch")
  library("kableExtra")
  library("vioplot")
  library("WGCNA")
})

#source("meth_functions.R")

Load data

Load the annotation data and the Epic methylation data.

This analysis is to be conducted on Ubuntu with R4.

ann = getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b2.hg19)

ann_sub = ann[,c("chr","pos","strand","Name","Islands_Name",
    "Relation_to_Island","UCSC_RefGene_Name","UCSC_RefGene_Group")]

targets_gen = read.metharray.sheet(dataDir, pattern = "CHART_sample_sheet_adults.csv")
## [read.metharray.sheet] Found the following CSV files:
## [1] "/analysis/him_chart_idats/CHART_idats/CHART_sample_sheet_adults.csv"
#targets$ID = paste(targets$Sample_Group,targets_gen$Sample_Name,sep=".")
rgSet = read.metharray.exp(targets = targets_gen)
## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls

## Warning in readChar(con, nchars = n): truncating string with embedded nuls
sampleNames(rgSet) = targets_gen$sample_id

rgSet$Slide <- as.numeric(rgSet$Slide)
rgSet$gender_m_f <- as.character(rgSet$gender_m_f)
rgSet$Sex <- as.character(rgSet$gender_m_f)
rgSet$sample_id <- as.character(rgSet$sample_id)


targets_gen$gender_m_f <- factor(targets_gen$gender_m_f)
targets_gen$status <- factor(targets_gen$status,levels=c("control","case"))
targets_gen$birth <- factor(targets_gen$birth,levels=c("Vaginal","Elective caesarian","Emergency caesarean"))
targets_gen$gest <- as.numeric(targets_gen$gest)
## Warning: NAs introduced by coercion
targets_gen$sga2 <-  factor(paste(targets_gen$sga,targets_gen$lrga),levels=c("Not small for gestational age - above 10th percentile Large for gestational age - above 90th percentile","Not small for gestational age - above 10th percentile Not large for gestational age - below 90th percentile","Small for gestational age - below 10th percentile Not large for gestational age - below 90th percentile"))

Testing familial structure

snpBetas = getSnpBeta(rgSet)
## Loading required package: IlluminaHumanMethylationEPICmanifest
d = dist(t(snpBetas))
hr = hclust(d, method = "complete", members=NULL)
plot(hr)