## ----echo = FALSE------------------------------------------------------------- knitr::opts_chunk$set(collapse=TRUE, comment='#>') ## ----read_tcga, message=F, warning=F------------------------------------------ library(minfi) library(conumee) library(minfiData) data(RGsetEx) sampleNames(RGsetEx) <- pData(RGsetEx)$Sample_Name cancer <- pData(RGsetEx)$status == 'cancer' RGsetEx <- RGsetEx[,cancer] RGsetEx ## ----normalize_tcga----------------------------------------------------------- MsetEx <- preprocessIllumina(RGsetEx) MsetEx ## ----prepare_controls, message=F---------------------------------------------- library(CopyNeutralIMA) ima <- annotation(MsetEx)[['array']] RGsetCtrl <- getCopyNeutralRGSet(ima) # preprocess as with the sample data MsetCtrl <- preprocessIllumina(RGsetCtrl) MsetCtrl ## ----conumee------------------------------------------------------------------ # use the information provided by conumee to create annotation files or define # them according to the package instructions data(exclude_regions) data(detail_regions) anno <- CNV.create_anno(array_type = "450k", exclude_regions = exclude_regions, detail_regions = detail_regions) # load in the data from the reference and samples to be analyzed control.data <- CNV.load(MsetCtrl) ex.data <- CNV.load(MsetEx) cnv <- CNV.fit(ex.data["GroupB_1"], control.data, anno) cnv <- CNV.bin(cnv) cnv <- CNV.detail(cnv) cnv <- CNV.segment(cnv) cnv CNV.genomeplot(cnv) CNV.genomeplot(cnv, chr = 'chr18') head(CNV.write(cnv, what = 'segments')) head(CNV.write(cnv, what='probes')) ## ----session_info, echo = F--------------------------------------------------- sessionInfo()