Name Mode Size
..
AffineAlignObj-class.Rd 100644 1 kb
AffineAlignObjLight-class.Rd 100644 1 kb
AffineAlignObjMedium-class.Rd 100644 1 kb
AlignObj-class.Rd 100644 1 kb
DIAlignR.Rd 100644 0 kb
MSTperBatch.Rd 100644 2 kb
XIC_QFNNTDIVLLEDFQK_3_DIAlignR.Rd 100644 1 kb
addFlankToLeft.Rd 100644 1 kb
addFlankToRight.Rd 100644 1 kb
addXIC.Rd 100644 1 kb
alignChromatogramsCpp.Rd 100644 4 kb
alignObj_DIAlignR.Rd 100644 2 kb
alignTargetedRuns.Rd 100644 2 kb
alignToMaster.Rd 100644 4 kb
alignToRef.Rd 100644 2 kb
alignToRefMST.Rd 100644 2 kb
alignToRoot4.Rd 100644 1 kb
alignedXIC.Rd 100644 2 kb
alignmentStats.Rd 100644 1 kb
analytesFromFeatures.Rd 100644 1 kb
approxFill.Rd 100644 1 kb
areaIntegrator.Rd 100644 2 kb
as.list-AffineAlignObj-method.Rd 100644 1 kb
as.list-AffineAlignObjLight-method.Rd 100644 1 kb
as.list-AffineAlignObjMedium-method.Rd 100644 1 kb
as.list-AlignObj-method.Rd 100644 1 kb
blobXICs.Rd 100644 1 kb
calculateIntensity.Rd 100644 1 kb
checkOverlap.Rd 100644 1 kb
checkParams.Rd 100644 1 kb
childXIC.Rd 100644 3 kb
childXICs.Rd 100644 2 kb
chromatogramIdAsInteger.Rd 100644 1 kb
constrainSimCpp.Rd 100644 1 kb
createMZML.Rd 100644 1 kb
createSqMass.Rd 100644 2 kb
dialignrLoess.Rd 100644 1 kb
doAffineAlignmentCpp.Rd 100644 2 kb
doAlignmentCpp.Rd 100644 2 kb
extractXIC_group.Rd 100644 1 kb
extractXIC_group2.Rd 100644 1 kb
fetchAnalytesInfo.Rd 100644 3 kb
fetchFeaturesFromRun.Rd 100644 2 kb
fetchPeptidesInfo.Rd 100644 1 kb
fetchPeptidesInfo2.Rd 100644 1 kb
fetchPrecursorsInfo.Rd 100644 2 kb
fetchTransitionsFromRun.Rd 100644 2 kb
filenamesFromMZML.Rd 100644 1 kb
filenamesFromOSW.Rd 100644 1 kb
getAlignObj.Rd 100644 4 kb
getAlignObjs.Rd 100644 2 kb
getAlignedFigs.Rd 100644 2 kb
getAlignedIndices.Rd 100644 4 kb
getAlignedTimes.Rd 100644 4 kb
getAlignedTimesCpp.Rd 100644 4 kb
getAlignedTimesFast.Rd 100644 2 kb
getAnalytesQuery.Rd 100644 1 kb
getBaseGapPenaltyCpp.Rd 100644 1 kb
getChildFeature.Rd 100644 2 kb
getChildXICpp.Rd 100644 4 kb
getChildXICs.Rd 100644 3 kb
getChromSimMatCpp.Rd 100644 3 kb
getChromatogramIndices.Rd 100644 2 kb
getFeatures.Rd 100644 2 kb
getFeaturesQuery.Rd 100644 1 kb
getGlobalAlignMaskCpp.Rd 100644 2 kb
getGlobalAlignment.Rd 100644 1 kb
getGlobalFits.Rd 100644 2 kb
getLOESSfit.Rd 100644 1 kb
getLinearfit.Rd 100644 1 kb
getMST.Rd 100644 1 kb
getMZMLpointers.Rd 100644 1 kb
getMappedRT.Rd 100644 4 kb
getMultipeptide.Rd 100644 2 kb
getNativeIDs.Rd 100644 1 kb
getNodeIDs.Rd 100644 1 kb
getNodeRun.Rd 100644 4 kb
getOswAnalytes.Rd 100644 2 kb
getOswFiles.Rd 100644 3 kb
getPeptideQuery.Rd 100644 1 kb
getPeptideQuery2.Rd 100644 1 kb
getPeptideScores.Rd 100644 2 kb
getPrecursorByID.Rd 100644 2 kb
getPrecursorIndices.Rd 100644 2 kb
getPrecursorSubset.Rd 100644 1 kb
getPrecursors.Rd 100644 2 kb
getPrecursorsQuery.Rd 100644 1 kb
getPrecursorsQueryID.Rd 100644 1 kb
getQuery.Rd 100644 1 kb
getRSE.Rd 100644 1 kb
getRTdf.Rd 100644 1 kb
getRefRun.Rd 100644 1 kb
getRunNames.Rd 100644 1 kb
getSeqSimMatCpp.Rd 100644 1 kb
getTransitions.Rd 100644 2 kb
getTransitionsQuery.Rd 100644 1 kb
getTree.Rd 100644 1 kb
getXICs.Rd 100644 2 kb
getXICs4AlignObj.Rd 100644 2 kb
get_ropenms.Rd 100644 1 kb
imputeChromatogram.Rd 100644 1 kb
ipfReassignFDR.Rd 100644 1 kb
mapIdxToTime.Rd 100644 1 kb
mapPrecursorToChromIndices.Rd 100644 1 kb
mappedRTfromAlignObj.Rd 100644 1 kb
masterXICs_DIAlignR.Rd 100644 1 kb
mergeOswAnalytes_ChromHeader.Rd 100644 1 kb
mergeXIC.Rd 100644 2 kb
mstAlignRuns.Rd 100644 2 kb
mstScript1.Rd 100644 2 kb
mstScript2.Rd 100644 2 kb
multipeptide_DIAlignR.Rd 100644 1 kb
nrDesc.Rd 100644 1 kb
oswFiles_DIAlignR.Rd 100644 1 kb
otherChildXICpp.Rd 100644 2 kb
paramsDIAlignR.Rd 100644 6 kb
perBatch.Rd 100644 2 kb
pickNearestFeature.Rd 100644 2 kb
plotAlignedAnalytes.Rd 100644 1 kb
plotAlignmentPath.Rd 100644 1 kb
plotAnalyteXICs.Rd 100644 2 kb
plotSingleAlignedChrom.Rd 100644 1 kb
plotXICgroup.Rd 100644 1 kb
progAlignRuns.Rd 100644 3 kb
progComb3.Rd 100644 1 kb
progSplit2.Rd 100644 1 kb
progSplit4.Rd 100644 1 kb
progTree1.Rd 100644 1 kb
readMzMLHeader.Rd 100644 1 kb
readSqMassHeader.Rd 100644 1 kb
recalculateIntensity.Rd 100644 2 kb
reduceXICs.Rd 100644 1 kb
script1.Rd 100644 1 kb
script2.Rd 100644 2 kb
setAlignmentRank.Rd 100644 2 kb
sgolayCpp.Rd 100644 1 kb
sgolayFill.Rd 100644 1 kb
smoothSingleXIC.Rd 100644 2 kb
smoothXICs.Rd 100644 2 kb
splineFill.Rd 100644 1 kb
splineFillCpp.Rd 100644 1 kb
traverseDown.Rd 100644 4 kb
traverseMST.Rd 100644 1 kb
traverseUp.Rd 100644 4 kb
trfrParentFeature.Rd 100644 2 kb
trimXICs.Rd 100644 1 kb
uncompressVec.Rd 100644 1 kb
updateFileInfo.Rd 100644 1 kb
updateOnalignTargetedRuns.Rd 100644 1 kb
writeTables.Rd 100644 1 kb
readMzMLHeader.Rd
% Generated by roxygen2: do not edit by hand % Please edit documentation in R/read_mzml.R \name{readMzMLHeader} \alias{readMzMLHeader} \title{Get chromatogram header from a mzML file} \usage{ readMzMLHeader(mzmlName) } \arguments{ \item{mzmlName}{(char) path to xics file.} } \value{ (A data-frame) It has 10 columns. The two important columns are: \item{chromatogramId}{(integer) Fragment-ion ID that matches with transition ID in osw file.} \item{chromatogramIndex}{(integer) Index of chromatogram in mzML file.} } \description{ Get a table of chromatogram indices and respective transition IDs. } \examples{ dataPath <- system.file("extdata", package = "DIAlignR") mzmlName <-paste0(dataPath,"/xics/hroest_K120809_Strep0\%PlasmaBiolRepl2_R04_SW_filt.chrom.mzML") \dontrun{ chromHead <- readChromatogramHeader(mzmlName = mzmlName) } } \author{ Shubham Gupta, \email{shubh.gupta@mail.utoronto.ca} ORCID: 0000-0003-3500-8152 License: (c) Author (2019) + GPL-3 Date: 2019-12-13 } \keyword{internal}