## ----设置，包括= false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃if（！sireseenamespace（“ biocmanager”，悄悄= true）＃install.packages（“ Biocmanager”）＃Biocmanager :: install（“ Dialignr”）## ----------------------------------------------------------------------------------------------------------------------------------------------------库（Dialignr）## ---- getDatapath---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------结果= false = false = false，message = false，警告= false = false ----------------------------------------------------运行<-C（“ Hroest_k120809_strep0％plasmabiolrepl2_r04_sw_filt”，“ hroest_k120809_strep10％plasmabiolrepl2_r04_sw_filt”）参数[“上下文”]] < - “实验范围” ## ----结果= false，message = false，parning = false----------------------------------------------------------------------------------------------------------------------------------＃对于特定运行，提供了他们的名字。AlignTargetEdruns（datapath = datapath，outfile =“ test”，runs = runs，oswmerged = true，params = params = params）＃对于所有运行中的所有分析物，将它们保持为null。AlignTargetEdruns（datapath = datapath，outfile =“ test”，runs = null，oswmerged = true，params = params）## ----结果= false，message = false，message = false，palse = false = false------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- < - “ Run2 Run2 \ nrun1 Run0” Mstalignruns（datapath = datapath，outfile =“ test”，mstnet = tree，oswmerged = true，true，true，params = params）＃计算树在fly mstalignruns（datapath = datapath，outfile =“ test”，oswmerged = true，params = params）## ----结果= false，message = false，params = false = false = false----------------------------------------------------“（run1：0.08857142857，（run0：0.06857142857，run2：0.06857142857）MasterB：0.02）Master1;”progalignruns（datapath = datapath，outFile =“ test”，newicktree = text1，oswmerged = true，params = params）＃compute compute recute the the-fly progalignruns（datapath = datapath = datapath，outfile =“ offile =“ test”，oswmerged = true = true，params = trams =参数）## ----消息= false ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") AlignObjLight <- getAlignObjs(analytes = 4618L, runs = runs, dataPath = dataPath, objType = "light", params = params) # First element contains names of runs, spectra files, chromatogram files and feature files. AlignObjLight[[1]][, c("runName", "spectraFile")] obj <- AlignObjLight[[2]][["4618"]][[1]][["AlignObj"]] slotNames(obj) names(as.list(obj)) AlignObjMedium <- getAlignObjs(analytes = 4618L, runs = runs, dataPath = dataPath, objType = "medium", params = params) obj <- AlignObjMedium[[2]][["4618"]][[1]][["AlignObj"]] slotNames(obj) ## ---- fig.width=6, fig.align='center', fig.height=6, message=FALSE------------ runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") AlignObj <- getAlignObjs(analytes = 4618L, runs = runs, dataPath = dataPath, params = params) plotAlignedAnalytes(AlignObj, annotatePeak = TRUE) ## ---- fig.width=5, fig.align='center', fig.height=5, message=FALSE------------ library(lattice) runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") AlignObjOutput <- getAlignObjs(analytes = 4618L, runs = runs, params = params, dataPath = dataPath, objType = "medium") plotAlignmentPath(AlignObjOutput) ## ----------------------------------------------------------------------------- sessionInfo()