## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----message=FALSE, xcms------------------------------------------------------ library(cliqueMS) mzfile <- system.file("standards.mzXML", package = "cliqueMS") library(xcms) mzraw <- readMSData(files = mzfile, mode = "onDisk") cpw <- CentWaveParam(ppm = 15, peakwidth = c(5,20), snthresh = 10) mzData <- findChromPeaks(object = mzraw, param = cpw) ## ----anclique----------------------------------------------------------------- ex.anClique <- createanClique(mzData) show(ex.anClique) ## ----cliquefind, include = TRUE----------------------------------------------- set.seed(2) ex.cliqueGroups <- getCliques(mzData, filter = TRUE) show(ex.cliqueGroups) ## ----isotopes, include = TRUE------------------------------------------------- ex.Isotopes <- getIsotopes(ex.cliqueGroups, ppm = 10) show(ex.Isotopes) ## ----positive, include = TRUE------------------------------------------------- data(positive.adinfo) head(positive.adinfo) data(negative.adinfo) head(negative.adinfo) ## ----adducts, include = TRUE-------------------------------------------------- ex.Adducts <- getAnnotation(ex.Isotopes, ppm = 10, adinfo = positive.adinfo, polarity = "positive", normalizeScore = TRUE) show(ex.Adducts) ## ----peaklist, include = TRUE------------------------------------------------- features.clique6 <- getlistofCliques(ex.Adducts)[[6]] head(getPeaklistanClique(ex.Adducts)[features.clique6, c("an1","mass1","an2", "mass2", "an3", "mass3", "an4", "mass4", "an5", "mass5")], n = 10)