## ----knitr, include=FALSE, echo=FALSE------------------------------------ library(knitr) opts_chunk$set(tidy=FALSE,size='scriptsize', cache=FALSE, cache.comments=FALSE) ## ----options,eval=TRUE,echo=FALSE,results='hide'-------------------- options(width=70) ## ----install, eval=FALSE-------------------------------------------- # packages.install('mixsmsn') # source('http://bioconductor.org/biocLite.R') # biocLite(c('skewr', 'methylumi', 'minfi', 'wateRmelon', # 'IlluminaHumanMethylation450kmanifest', 'IRanges')) ## ----minfiData, eval=FALSE------------------------------------------ # biocLite('minfiData') ## ----load, message=FALSE, warning=FALSE----------------------------- library(skewr) library(minfiData) ## ----getIDATs, eval=TRUE, warning=FALSE, message=FALSE-------------- baseDir <- system.file("extdata/5723646052", package = "minfiData") barcodes <- getBarcodes(path = baseDir) barcodes ## ----getMethyLumi, eval=FALSE, warning=FALSE, message=FALSE--------- # methylumiset.raw <- getMethyLumiSet(path = baseDir, barcodes = barcodes[1:2]) # methylumiset.illumina <- preprocess(methylumiset.raw, norm = 'illumina', # bg.corr = FALSE) ## ----getMelon, eval=TRUE-------------------------------------------- data(melon) melon.raw <- melon[,11] ## ----getMethyLumiNormEx, eval=FALSE--------------------------------- # melon.illumina <- preprocess(melon.raw, norm = 'illumina', bg.corr = TRUE) # melon.SWAN <- preprocess(melon.raw, norm = 'SWAN') # melon.dasen <- preprocess(melon.raw, norm = 'dasen') ## ----mixes, eval=TRUE----------------------------------------------- sn.raw.meth.I.red <- getSNparams(melon.raw, 'M', 'I-red') sn.raw.unmeth.I.red <- getSNparams(melon.raw, 'U', 'I-red') sn.raw.meth.I.green <- getSNparams(melon.raw, 'M', 'I-green') sn.raw.unmeth.I.green <- getSNparams(melon.raw, 'U', 'I-green') sn.raw.meth.II <- getSNparams(melon.raw, 'M', 'II') sn.raw.unmeth.II <- getSNparams(melon.raw, 'U', 'II') ## ----mixesdasen, eval=FALSE----------------------------------------- # sn.dasen.meth.I.red <- getSNparams(melon.dasen, 'M', 'I-red') # sn.dasen.unmeth.I.red <- getSNparams(melon.dasen, 'U', 'I-red') # sn.dasen.meth.I.green <- getSNparams(melon.dasen, 'M', 'I-green') # sn.dasen.unmeth.I.green <- getSNparams(melon.dasen, 'U', 'I-green') # sn.dasen.meth.II <- getSNparams(melon.dasen, 'M', 'II') # sn.dasen.unmeth.II <- getSNparams(melon.dasen, 'U', 'II') ## ----list, eval=TRUE------------------------------------------------ raw.I.red.mixes <- list(sn.raw.meth.I.red, sn.raw.unmeth.I.red) raw.I.green.mixes <- list(sn.raw.meth.I.green, sn.raw.unmeth.I.green) raw.II.mixes <- list(sn.raw.meth.II, sn.raw.unmeth.II) ## ----panelPlot1, eval=TRUE, echo=TRUE, dev='png', dpi=300, fig.cap='Panel Plot for One Sample'---- panelPlots(melon.raw, raw.I.red.mixes, raw.I.green.mixes, raw.II.mixes, norm = 'Raw') ## ----panelPlot2, eval=FALSE, echo=TRUE, dev='png', dpi=600---------- # panelPlots(melon.dasen, # list(sn.dasen.meth.I.red, sn.dasen.unmeth.I.red), # list(sn.dasen.meth.I.green, sn.dasen.unmeth.I.green), # list(sn.dasen.meth.II, sn.dasen.unmeth.II), norm = 'dasen') ## ----listAccess, eval=TRUE------------------------------------------ class(sn.raw.meth.I.red[[1]]) names(sn.raw.meth.I.red[[1]]) sn.raw.meth.I.red[[1]]$means sn.raw.meth.I.red[[1]]$modes ## ----singlePlots, eval=TRUE, echo=TRUE, dev='png', dpi=300, fig.cap=c('Single Frame Showing Skew-normal Components', 'Single Frame Showing Beta Distribution for Type I Red')---- panelPlots(melon.raw, raw.I.red.mixes, raw.I.green.mixes, raw.II.mixes, plot='frames', frame.nums=c(1,3), norm='Raw') ## ----sessionInfo, results='asis', echo=FALSE------------------------ toLatex(sessionInfo())