## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----setup, include=FALSE----------------------------------------------------- options(width = 80) require(knitr) opts_chunk$set(dev='png', prompt=TRUE, comment=NA, tidy=FALSE) ## ----readFiles, warning=FALSE, message=FALSE---------------------------------- library(rCGH) filePath <- system.file("extdata", "Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2", package = "rCGH") cgh <- readAffyCytoScan(filePath, sampleName = "CSc-Example", labName = "myLab") ## ----cgh, warning=FALSE, message=FALSE---------------------------------------- cgh ## ----addInfo------------------------------------------------------------------ setInfo(cgh, "item1") <- 35 setInfo(cgh, "item2") <- TRUE setInfo(cgh, "item3") <- "someComment" ## ----getInfo------------------------------------------------------------------ getInfo(cgh) getInfo(cgh, c("item1", "item3")) ## ----adjustSignal------------------------------------------------------------- cgh <- adjustSignal(cgh, nCores=1) ## ----SegmentCGH--------------------------------------------------------------- cgh <- segmentCGH(cgh, nCores=1) segTable <- getSegTable(cgh) ## ----segTable----------------------------------------------------------------- head(segTable) ## ----EMnormalize-------------------------------------------------------------- cgh <- EMnormalize(cgh) ## ----plotDensity, fig.width=7, fig.height=5, fig.show='hide'------------------ plotDensity(cgh) ## ----byGeneTable-------------------------------------------------------------- geneTable <- byGeneTable(segTable) head(geneTable, n=3) ## ----byGeneTable2------------------------------------------------------------- byGeneTable(segTable, "erbb2", genome = "hg19")[,1:6] byGeneTable(segTable, "erbb2", genome = "hg18")[,1:6] ## ----getParams---------------------------------------------------------------- getParam(cgh)[1:3] ## ----getProfile, fig.width=7.7, fig.height=9.5, fig.show='hide'--------------- multiplot(cgh, symbol = c("egfr", "erbb2")) ## ----recenter, fig.width=7.5, fig.height=4, fig.show='hide'------------------- # Recentering on peak #2 recenter(cgh) <- 2 plotProfile(cgh, symbol = c("egfr", "erbb2")) ## ----view, eval=FALSE, echo=TRUE---------------------------------------------- # view(cgh) ## ----exampleFiles------------------------------------------------------------- list.files(system.file("extdata", package = "rCGH")) ## ----session------------------------------------------------------------------ sessionInfo()