## ----results='hide'， message=FALSE, warning=FALSE, echo = TRUE--------------- library(mspsecurity) library(xcms) mzMLpths <- list.files(system. files)file("extdata"， "lcms"， "mzML"， package="msPurityData")， full.names = TRUE) #read in the data xset = xcms::xcmsSet(mzMLpths, method = 'centWave'， mslevel=1, snthresh = 3, noise = 100, ppm = 10, peakwidth = c(3，30) #对于本例,我们将子集的数据集中保留时间范围30 - 90秒和扫描范围100 - 200 m / z xset@peaks = xset@peaks [xset@peaks [4] > = 30 & xset@peaks[4] < = 90] #保留时间过滤xset@peaks = xset@peaks [xset@peaks [1] > = 100 & xset@peaks [1] < = 200] # m / z过滤器#组特征在样本xset = xcms::集团(xset minfrac = 0, bw = 5, mzwid = 0.017) xcmsObj = xset # #——结果=“隐藏”,消息= FALSE,警告= FALSE,echo = TRUE--------------- library(mspsecurity) library(magrittr) library(xcms) library(MSnbase) mzMLpths <- list.files(system. base)file("extdata"， "lcms"， "mzML"， package="msPurityData")， full.names = TRUE) #读入数据和子集以使用30到90秒之间的数据和100和200 m/z msdata = readMSData(mzMLpths, mode = 'onDisk'， msLevel. properties)。= 1) rtr = c (90) mzr = c(100、200)msdata = msdata % > % MSnbase:: filterRt (rt = rtr) % > % MSnbase:: filterMz (mz = mzr) #在单个文件中执行功能检测cwp < - CentWaveParam (snthresh = 3,噪音= 100 ppm = 10, peakwidth = c (30)) xcmsObj < - xcms:: findChromPeaks (msdata参数= cwp) #更新元数据xcmsObj@phenoData@data $类= c(“空白”、“空白”、“样品”,“样本”)xcmsObj@phenoData@varMetadata = data.frame(“labelDescription”= c(“sampleNames”,'class')) #组色谱峰在样品(对应分析)pdp <- PeakDensityParam(sampleGroups = xcmsObj@phenoData@data$class, minFraction = 0, bw = 5, binSize = 0.017) xcmsObj <- groupChromPeaks(xcmsObj, param = pdp) ## ----results='hide'， message=FALSE, warning=FALSE, echo = TRUE--------------- pa <- purityA(mzMLpths) pa <- frag4feature(pa = pa, xcmmlpj = xcmsObj) ## ----results='hide'， message=FALSE, warning=FALSE，回声= TRUE --------------- pa < - filterFragSpectra (pa = pa) # #——结果=“隐藏”,消息= FALSE,警告= FALSE,回声= TRUE --------------- pa < - averageIntraFragSpectra (pa = pa) #使用参数特定于内部光谱pa <——averageInterFragSpectra (pa = pa) #使用参数特定于国米光谱# # =“隐藏”——结果,消息= FALSE,警告= FALSE,回声= TRUE --------------- pa < - averageAllFragSpectra (pa = pa) # #——结果=“隐藏”,消息= FALSE,警告= FALSE,回声= TRUE --------------- td < - tempdir () q_dbPth < - createDatabase (pa = pa, xcmsObj = xcmsObj outDir = td, dbName = ' lcmsms-processing.sqlite ') ## ----------------------------------------------------------------------------- 结果< - spectralMatching (q_dbPth q_xcmsGroups = c (432), l_accessions = c (CCMSLIB00003740033))打印(结果)