## ---- echo = TRUE, collapse = TRUE, results = 'markup'， warning = FALSE, message = FALSE---- library("minfi") library("conumee") #RGsetTCGA <- read.450k。exp(base = "~/conumee_analysis/ jgu -usc. edu_brca . humanmethylation450 . level_8.8.0 ") #调整路径RGsetTCGA <- read.450k.url() #使用默认参数为插图示例MsetTCGA <- preprocessIllumina(RGsetTCGA) MsetTCGA ## ---- echo = TRUE, collapse = TRUE, results = 'markup'， warning = FALSE, message = FALSE---- library("minfiData") data(MsetEx) MsetEx ## ---- echo = TRUE, collapse = TRUE, results = 'markup'， warning = FALSE, warning = FALSE，message = FALSE---- # library("CopyNumber450kData") # data(RGcontrolSetEx) # MsetControls <- preprocessIllumina(RGcontrolSetEx) ## ---- echo = TRUE, collapse = TRUE, results = 'markup'， warning = TRUE, message = TRUE---- data(exclude_regions) data(detail_regions) head(detail_regions, n = 2) anno <- CNV。create_anno(array_type = "450k"， exclude_regions = exclude_regions, detail_regions = detail_regions) anno ## ---- echo = TRUE, collapse = TRUE, results = 'markup'， warning = FALSE, message = FALSE---- data(tcgaBRCA.sentrix2name) # TCGA示例id随conumee包sampleNames(MsetTCGA) <- tcgaBRCA.sentrix2name[sampleNames(MsetTCGA)] TCGA提供。data <- CNV.load(MsetTCGA) tcga。controls <- grep("- 11a -"， names(tcga.data)) names(tcga.data)minfi数据。data <- CNV.load(MsetEx)控件<- pData(MsetEx)$status == "normal" #控件。data <- CNV.load(MsetControls) ## ---- echo = TRUE, collapse = TRUE, results = 'markup'， warning = FALSE, message = FALSE---- x <- CNV.fit(minfi. fit)。数据(“GroupB_1”),minfi.data [minfi。control]， anno) # y <- CNV.fit(tcga。数据(“TCGA-AR-A1AU-01A-11D-A12R-05”),控件。data, anno) # CopyNumber450kData package is deprecated # z <- CNV.fit(tcga.data["TCGA-AR-A1AY-01A-21D-A12R-05"], controls.data, anno) y <- CNV.fit(tcga.data["TCGA-AR-A1AU-01A-11D-A12R-05"], minfi.data[minfi.controls], anno) # minfiData control samples z <- CNV.fit(tcga.data["TCGA-AR-A1AY-01A-21D-A12R-05"], minfi.data[minfi.controls], anno) x <- CNV.bin(x) x <- CNV.detail(x) x <- CNV.segment(x) y <- CNV.segment(CNV.detail(CNV.bin(y))) z <- CNV.segment(CNV.detail(CNV.bin(z))) x ## ---- echo = TRUE, fig.show = 'hold', collapse = TRUE, results = 'markup', warning = FALSE, message = FALSE, fig.width = 14, fig.height = 7, out.width = "800px", fig.retina = 1---- #pdf("~/conumee_analysis/CNVplots.pdf", height = 9, width = 18) CNV.genomeplot(x) CNV.genomeplot(y) CNV.genomeplot(y, chr = "chr6") CNV.genomeplot(z) CNV.genomeplot(z, chr = "chr10") CNV.detailplot(z, name = "PTEN") CNV.detailplot_wrap(z) #dev.off() head(CNV.write(y, what = "segments"), n = 5) #CNV.write(y, what = "segments", file = "~/conumee_analysis/TCGA-AR-A1AU.CNVsegments.seg") # adjust path #CNV.write(y, what = "bins", file = "~/conumee_analysis/TCGA-AR-A1AU.CNVbins.igv") #CNV.write(y, what = "detail", file = "~/conumee_analysis/TCGA-AR-A1AU.CNVdetail.txt") #CNV.write(y, what = "probes", file = "~/conumee_analysis/TCGA-AR-A1AU.CNVprobes.igv") ## ---- echo = TRUE, collapse = TRUE, results = 'markup', warning = FALSE, message = FALSE---- citation("conumee") ## ---- echo = TRUE, collapse = TRUE, results = 'markup', warning = FALSE, message = FALSE---- sessionInfo()