Nothing
## ----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()
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