### R code from vignette source 'read_and_normalize450K.Rnw' ################################################### ### code chunk number 1: read_and_normalize450K.Rnw:17-31 (eval = FALSE) ################################################### ## library(normalize450K) ## library(minfiData) ## this package includes some .idat files ## library(data.table) ## ## path <- system.file("extdata",package="minfiData") ## samples = fread(file.path(path, 'SampleSheet.csv'),integer64='character') ## ## samples[,file:=file.path(path,Sentrix_ID,paste0(Sentrix_ID,'_',Sentrix_Position))] ## ## samples$file is a character vector containing the location of the ## ## .idat files, but without the suffixes "_Red.idat" or "_Grn.idat" ## ## raw = read450K(samples$file) ## none = dont_normalize450K(raw) ## no normalization ## norm = normalize450K(raw)