## ----dependencies, warning=FALSE, message=FALSE-------------------------- library(minfi) library(GEOquery) ## ----biocLite, eval=FALSE------------------------------------------------ ## source("http://www.bioconductor.org/biocLite.R") ## biocLite(c("minfi", "GEOquery")) ## ----geoquery------------------------------------------------------------ library(GEOquery) getGEOSuppFiles("GSE68777") untar("GSE68777/GSE68777_RAW.tar", exdir = "GSE68777/idat") head(list.files("GSE68777/idat", pattern = "idat")) ## ----decompress---------------------------------------------------------- idatFiles <- list.files("GSE68777/idat", pattern = "idat.gz$", full = TRUE) sapply(idatFiles, gunzip, overwrite = TRUE) ## ----readExp------------------------------------------------------------- rgSet <- read.450k.exp("GSE68777/idat") rgSet pData(rgSet) head(sampleNames(rgSet)) ## ----geoPheno------------------------------------------------------------ geoMat <- getGEO("GSE68777") pD.all <- pData(geoMat[[1]]) pD <- pD.all[, c("title", "geo_accession", "characteristics_ch1.1", "characteristics_ch1.2")] head(pD) names(pD)[c(3,4)] <- c("group", "sex") pD$group <- sub("^diagnosis: ", "", pD$group) pD$sex <- sub("^Sex: ", "", pD$sex) ## ----merge--------------------------------------------------------------- sampleNames(rgSet) <- sub(".*_5", "5", sampleNames(rgSet)) rownames(pD) <- pD$title pD <- pD[sampleNames(rgSet),] pData(rgSet) <- pD rgSet ## ----preprocess---------------------------------------------------------- grSet <- preprocessQuantile(rgSet) grSet ## ----granges------------------------------------------------------------- granges(grSet) ## ----getBeta------------------------------------------------------------- getBeta(grSet)[1:3,1:3] ## ----getIslandStatus----------------------------------------------------- head(getIslandStatus(grSet)) ## ----sessionInfo, echo=FALSE--------------------------------------------- sessionInfo()