## ------------------------------------------------------------------------ library(msPurity) msmsPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "MSMS") msPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "LCMS_") ## ------------------------------------------------------------------------ pa <- purityA(msmsPths) print(head(pa@puritydf)) ## ------------------------------------------------------------------------ library(xcms) xset <- xcms::xcmsSet(msmsPths) xset <- xcms::group(xset) xset <- xcms::retcor(xset) xset <- xcms::group(xset) ## ------------------------------------------------------------------------ pa <- frag4feature(pa, xset) ## ------------------------------------------------------------------------ print(head(pa@grped_df)) ## ------------------------------------------------------------------------ print(pa@grped_ms2[2:3]) ## ------------------------------------------------------------------------ xset <- xcms::xcmsSet(msPths) xset <- xcms::group(xset) xset <- xcms::retcor(xset) xset <- xcms::group(xset) ## ------------------------------------------------------------------------ ppLCMS <- purityX(xset, offsets=c(0.5, 0.5), xgroups = c(1, 2)) print(head(ppLCMS@predictions)) ## ------------------------------------------------------------------------ datapth <- system.file("extdata", "dims", "mzML", package="msPurityData") inDF <- Getfiles(datapth, pattern=".mzML", check = FALSE) ppDIMS <- purityD(inDF, mzML=TRUE) ## ------------------------------------------------------------------------ ppDIMS <- averageSpectra(ppDIMS, snMeth = "median", snthr = 5) ## ------------------------------------------------------------------------ ppDIMS <- filterp(ppDIMS, thr=5000, rsd = 10) ## ------------------------------------------------------------------------ ppDIMS <- subtract(ppDIMS) ## ------------------------------------------------------------------------ ppDIMS <- dimsPredictPurity(ppDIMS) print(head(ppDIMS@avPeaks$processed$B02_Daph_TEST_pos)) ## ------------------------------------------------------------------------ mzpth <- system.file("extdata", "dims", "mzML", "B02_Daph_TEST_pos.mzML", package="msPurityData") predicted <- dimsPredictPuritySingle(filepth = mzpth, mztargets = c(111.0436, 113.1069)) print(predicted)