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1_Eye_Methylation_Preprocessing.R
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#############################################################
#source("https://bioconductor.org/biocLite.R")
#biocLite("minfi")
#biocLite("IlluminaHumanMethylation450kmanifest")
#############################################################
library(minfi)
rgset<- read.450k.exp("~/Desktop/Research/AMD/Methylation/EyeBank/Data/raw/Eye Methylation Project/")
rgset
pData(rgset)
head(sampleNames(rgset))
beta.table<-getBeta(rgset)
colnames(beta.table)
# Sample Mapping
# Sentrix_ID_Position ID
# 6042308131_R01C01 = 3631B
# 6042308131_R01C02 = 3675O
# 6042308131_R02C01 = 3631C
# 6042308131_R02C02 = 3675R
# 6042308131_R03C01 = 3631O
# 6042308131_R03C02 = 3677B
# 6042308131_R04C01 = 3631R
# 6042308131_R04C02 = 3677C
# 6042308131_R05C01 = 3675B
# 6042308131_R05C02 = 3677O
# 6042308131_R06C01 = 3675C
# 6042308131_R06C02 = 3677R
# 6042308133_R01C01 = 3684B
# 6042308133_R01C02 = 3685O
# 6042308133_R02C01 = 3684C
# 6042308133_R02C02 = 3685R
# 6042308133_R03C01 = 3684O
# 6042308133_R03C02 = 3689B
# 6042308133_R04C01 = 3684R
# 6042308133_R04C02 = 3689C
# 6042308133_R05C01 = 3685B
# 6042308133_R05C02 = 3689O
# 6042308133_R06C01 = 3685C
# 6042308133_R06C02 = 3689R
# 6042308134_R01C01 = 3682C
# 6042308134_R02C01 = 3682O
# 6042308134_R03C01 = 3682R
# 6042308134_R04C01 = 3701R
# 6042308134_R05C01 = 3701B
colnames(beta.table) <- c("3631B","3675O","3631C","3675R","3631O","3677B","3631R","3677C","3675B","3677O","3675C","3677R","3684B","3685O","3684C","3685R","3684O","3689B","3684R","3689C","3685B","3689O","3685C","3689R","3682C","3682O","3682R","3701R","3701B")
write.csv(beta.table,"eyebetas.csv", row.names = TRUE)