## ----style, echo = FALSE, results = 'asis'--------------------------------- BiocStyle::markdown() ## ----echo = FALSE, results = "hide", message = FALSE----------------------- library(BiocStyle) ## ----load-libs, message = FALSE-------------------------------------------- library(xcms) library(msdata) ## Disable parallel processing register(SerialParam()) ## ----raw-files------------------------------------------------------------- mzdatapath <- system.file("iontrap", package = "msdata") list.files(mzdatapath, recursive = TRUE) ## -------------------------------------------------------------------------- library(xcms) mzdatafiles <- list.files(mzdatapath, pattern = "extracted.mzData", recursive = TRUE, full.names = TRUE) xraw <- xcmsRaw(mzdatafiles[1], includeMSn=TRUE) xraw ## -------------------------------------------------------------------------- peaks <- findPeaks(xraw, method="MS1") ## -------------------------------------------------------------------------- xs <- xcmsSet(mzdatafiles, method = "MS1") xfrag <- xcmsFragments(xs) xfrag ## -------------------------------------------------------------------------- plotTree(xfrag, xcmsFragmentPeakID = 6, textOnly = TRUE)