## ----environment, echo=FALSE-------------------------------------------------- suppressPackageStartupMessages(library("synapter")) suppressPackageStartupMessages(library("synapterdata")) suppressPackageStartupMessages(library("BiocStyle")) synobj2RData() ## ----create-synobj2-file, echo=FALSE, comment=NA------------------------------ cat(readLines(system.file(file.path("scripts", "create_synobj2.R"), package="synapterdata"), n=13), sep="\n") ## ----show-synobj2------------------------------------------------------------- synobj2 ## ----filtering---------------------------------------------------------------- filterUniqueDbPeptides(synobj2, missedCleavages=0, IisL=TRUE) filterPeptideLength(synobj2, l=7) plotFdr(synobj2) filterQuantPepScore(synobj2, method="BH", fdr=0.05) filterIdentPepScore(synobj2, method="BH", fdr=0.05) par(mfcol=c(1, 2)) plotPpmError(synobj2, what="Ident") plotPpmError(synobj2, what="Quant") par(mfcol=c(1, 1)) filterQuantPpmError(synobj2, ppm=20) filterIdentPpmError(synobj2, ppm=20) plotPepScores(synobj2) filterIdentProtFpr(synobj2, fpr=0.05) filterQuantProtFpr(synobj2, fpr=0.05) ## ----rtmodel------------------------------------------------------------------ mergePeptides(synobj2) plotRt(synobj2, what="data") setLowessSpan(synobj2, span=0.05) modelRt(synobj2) par(mfcol=c(1, 2)) plotRtDiffs(synobj2) plotRt(synobj2, what="model", nsd=1) par(mfcol=c(1, 1)) plotFeatures(synobj2, what="all", ionmobility=TRUE) ## ----gridsearch--------------------------------------------------------------- searchGrid(synobj2, imdiffs=seq(from=0.6, to=1.6, by=0.2), ppms=seq(from=2, to=20, by=2), nsds=seq(from=0.5, to=5, by=0.5)) setBestGridParams(synobj2) findEMRTs(synobj2) plotEMRTtable(synobj2) ## ----filterfragments---------------------------------------------------------- filterFragments(synobj2, what="fragments.ident", minIntensity=70) filterFragments(synobj2, what="spectra.quant", minIntensity=70) ## ----fm----------------------------------------------------------------------- fragmentMatching(synobj2) ## ----fmperf, results="asis"--------------------------------------------------- knitr::kable(fragmentMatchingPerformance(synobj2, what="unique")) knitr::kable(fragmentMatchingPerformance(synobj2, what="non-unique")) ## ----filterfm----------------------------------------------------------------- filterUniqueMatches(synobj2, minNumber=1) filterNonUniqueMatches(synobj2, minDelta=2) filterNonUniqueIdentMatches(synobj2) ## ----rescue------------------------------------------------------------------- rescueEMRTs(synobj2, method="rescue") ## ----intmodel----------------------------------------------------------------- plotIntensity(synobj2, what="data") setLowessSpan(synobj2, 0.05) modelIntensity(synobj2) plotIntensity(synobj2, what="model", nsd=1) ## ----synergise2, eval=FALSE--------------------------------------------------- # synobj2 <- synergise2(filenames = inlist, # outputdir = ".") ## ----convert------------------------------------------------------------------ msn <- as(synobj2, "MSnSet") ## ----synapterplgs, results="asis"--------------------------------------------- msn <- synapterPlgsAgreement(msn) knitr::kable(head(fData(msn)[, grepl("[Aa]gree", fvarLabels(msn)), drop=FALSE])) ## ----saturation--------------------------------------------------------------- msncor <- requantify(msn, saturationThreshold=1e5, method="sum") ## ----rescaletop3-------------------------------------------------------------- msncor <- rescaleForTop3(before=msn, after=msncor, saturationThreshold=1e5) ## ----sessioninfo-------------------------------------------------------------- sessionInfo()