## ----results='hide', message=FALSE, warning=FALSE, echo = TRUE--------------- library(msPurity) library(xcms) mzMLpths <- list。'，mslevel = 1，snthresh = 3，噪声= 100，ppm = 10，peakWidth = c（3，30））＃对于此示例，我们将将数据集中到保留时间范围30-90秒，并扫描范围100-200 m/z xset@peacs = xset@peacs [xset@peacs [，4]> = 30＆xset@peacs [，4] <= 90，] #retention tirention firtil filter xset@peacs = xset@peacs [xset@peacs@peacs@peacs@峰[，1]> = 100＆xset@peacs [，1] <= 200，]＃m/z滤波器#group profter profe xsem xset = xcms :: group（xset，minfrac = 0，bw = 5，mzwid = 5，mzwid =0.017) xcmsObj = xset ## ----results='hide', message=FALSE, warning=FALSE, echo = TRUE--------------- library(msPurity) library(magrittr）库（XCMS）库（msnbase）mzmlpths < - list.files（system.file（“ extdata”，“ lcms”，“ mzml”，“ mzml”，package =“ mspuritydata”），full.names = true）＃在数据和子集中读取的数据，以使用30至90秒之间的数据，100和200 m/z msdata = readmsdata（mzmlpths，mode，mode ='ondisk'，mslevel。= 1）rtr = c（30，90）mzr = c（100，200）msdata = msdata％>％msnbase :: filterrt（rt = rtr）％>％msnbase :: filtermz（mz = mzr）在单个文件中cwp <-centwaveParam（snthresh = 3，噪声= 100，ppm = 10，peakWidth = c（3，30））xcmsobj <-xcms :: findchrompeaks（msdata，param = cwp）data $ class = c（'空白'，'空白'，'sample'，'sample'）xcmsobj@phenodata@varmetadata = data.frame（'labEldescription'= c（'samplenames'，'class'，'class'）#group色谱跨样品（通讯分析）PDP <-peak-DensityParam（sampleGroups = XCMSOBJ@PENODATA@data $ class，minfraction = 0，bw = 5，binsize = 0.017）XCMSOBJ <-groupChrompeaks（XCMSOBJ，XCMSOBJ，XCMSOBJ，PARM = PDP）#-----results ='hide'，message = false，parning = false，echo = true ---------------------------------- pa <-puritya（mzmlpths）pa < - frag4feature（pa = pa，xcmsobj）= xcmsObj) ## ----results='hide', message=FALSE, warning=FALSE, echo = TRUE--------------- pa <- filterFragSpectra(pa = pa) ## ----results='hide', message=FALSE, warning=FALSE, echo = TRUE--------------- pa <- averageIntraFragSpectra(pa = pa) # use parameters specific to intra spectra pa <- averageInterFragSpectra(pa = pa) # use parameters specific to inter spectra ## ----results='hide', message=FALSE, warning=FALSE, echo = TRUE--------------- pa <- averageAllFragSpectra(pa = pa) ## ----results='hide', message=FALSE, warning=FALSE, echo = TRUE--------------- td <- tempdir() q_dbPth <- createDatabase(pa = pa, xcmsObj = xcmsObj, outDir = td, dbName = 'lcmsms-processing.sqlite') ## ----------------------------------------------------------------------------- result <- spectralMatching(q_dbPth, q_xcmsGroups = c(432), l_accessions=c('CCMSLIB00003740033')) print(result)