Man pages for thomasp85/MSsary
LC-MS/MS analysis in R

annotateChildrenCreate a data.frame with precursor scans
binIonsCreate profile data from ions
callToStringDeparse call into a single text string
chromsExtract chromatograms from an object
chroms-MsData-methodExtract chromatograms from an MsData object
chroms-MsIonList-methodExtract chromatograms from an ion list
chroms-MsPeakList-methodGet chroms with optional expansion
chroms-MsScanList-methodGet chroms with optional expansion
conGet the MsConnections object
createMsDataCreate an MsData object from a raw MS data file
createMsDataSetCreate an MsDataSet from a list of raw files
detectPeaksDetect peaks in chromatographic MS data
detectPeaks-MsData-methodPeak detection in MsData object
dropEmptySubsets an object to remove empty elements
editHistoryGet a list of all edits on an object
expand.callReturn a call in which all of the arguments which were...
fillGapsInterpolate gaps between RT bins
findGapsFind gaps in RT bins
getContAcqNumExtract a continuous range of acquisitionNums from the same...
getMzrPathExtract mzR file location from sary file
getPeakIdsGet peakIDs based on a filter
ionsExtract ions from an object
ions-MsChromList-methodExtract ions from the EIC
ions-MsData-methodExtract ions from an MsData object
ions-MsPeakList-methodGet ions with optional expansion
ions-MsScanList-methodGet ions with optional expansion
isEmptyTest whether the elements of an object are empty
isRawTest whether the elements of an object are based on raw value
loadMsDataLoad in an already created sary file as an MsData object
loadMsDataSetLoad an already created MsDataSet from a saryset file
massifquantRuns the massifquant algorithm
meltMSCreate ggplot2 ready data from object
methodStore-classObject to handle all peak detection methods
MsChromList-classClass to handle extracted ion chromatograms
MsConnections-classA class to handle MS I/O
MsData-classMain class for interacting with MS data
MsDataSet-classStore and operate on sets of samples
MsIonList-classClass to handle raw ion reads
MsList-accessorsMethods for accessing data in MsList objects
MsList-classVirtual class for MSsary list like objects
MsPeakList-classClass to handle detected peaks
msPlotGeneric plot function for MSsary objects
MSsary-packageMSsary: Easy handling of LC-MS/MS data in R
MsScanList-classClass to handle specific scans
MsScanList-navigatorsMethods for navigating scans
MsSet-classClass to handle MsSet connection
peakMethodStore-classObject to handle all peak detection methods
peaksExtract peaks from an object
peaks-MsChromList-methodExtract peaks from the EIC
peaks-MsData-methodExtrack peaks from an MsData object
peaks-MsIonList-methodExtract peaks from an MsIonList
peaks-MsScanList-methodGet peaks intersecting with scan
prepareMethodStore-classObject to handle all peak detection methods
prepareScansPreprocess scans
prepareScans-MsData-methodScan preprocessing in MsData objects
rbindGtableReplacement for the gtable rbind
scanModeGet and set the mode of scans in an MsScanList
scanNoiseGet intensity threshold for a given signal-to-noise ratio
scansExtract scans from an object
scans-MsChromList-methodExtract the scans that make up a chromatogram
scans-MsData-methodExtract scans from an MsData object
scans-MsIonList-methodExtract the scans that make up an ion list
scans-MsPeakList-methodGet scans from peak
uNamesGet unique names of elements
thomasp85/MSsary documentation built on May 31, 2019, 11:11 a.m.