MS analysis in R

annotateChildren	Create a data.frame with precursor scans
binIons	Create profile data from ions
callToString	Deparse call into a single text string
chroms	Extract chromatograms from an object
chroms-MsData-method	Extract chromatograms from an MsData object
chroms-MsIonList-method	Extract chromatograms from an ion list
chroms-MsPeakList-method	Get chroms with optional expansion
chroms-MsScanList-method	Get chroms with optional expansion
con	Get the MsConnections object
createMsData	Create an MsData object from a raw MS data file
createMsDataSet	Create an MsDataSet from a list of raw files
detectPeaks	Detect peaks in chromatographic MS data
detectPeaks-MsData-method	Peak detection in MsData object
dropEmpty	Subsets an object to remove empty elements
editHistory	Get a list of all edits on an object
expand.call	Return a call in which all of the arguments which were...
fillGaps	Interpolate gaps between RT bins
findGaps	Find gaps in RT bins
getContAcqNum	Extract a continuous range of acquisitionNums from the same...
getMzrPath	Extract mzR file location from sary file
getPeakIds	Get peakIDs based on a filter
ions	Extract ions from an object
ions-MsChromList-method	Extract ions from the EIC
ions-MsData-method	Extract ions from an MsData object
ions-MsPeakList-method	Get ions with optional expansion
ions-MsScanList-method	Get ions with optional expansion
isEmpty	Test whether the elements of an object are empty
isRaw	Test whether the elements of an object are based on raw value
loadMsData	Load in an already created sary file as an MsData object
loadMsDataSet	Load an already created MsDataSet from a saryset file
massifquant	Runs the massifquant algorithm
meltMS	Create ggplot2 ready data from object
methodStore-class	Object to handle all peak detection methods
MsChromList-class	Class to handle extracted ion chromatograms
MsConnections-class	A class to handle MS I/O
MsData-class	Main class for interacting with MS data
MsDataSet-class	Store and operate on sets of samples
MsIonList-class	Class to handle raw ion reads
MsList-accessors	Methods for accessing data in MsList objects
MsList-class	Virtual class for MSsary list like objects
MsPeakList-class	Class to handle detected peaks
msPlot	Generic plot function for MSsary objects
MSsary-package	MSsary: Easy handling of LC-MS/MS data in R
MsScanList-class	Class to handle specific scans
MsScanList-navigators	Methods for navigating scans
MsSet-class	Class to handle MsSet connection
peakMethodStore-class	Object to handle all peak detection methods
peaks	Extract peaks from an object
peaks-MsChromList-method	Extract peaks from the EIC
peaks-MsData-method	Extrack peaks from an MsData object
peaks-MsIonList-method	Extract peaks from an MsIonList
peaks-MsScanList-method	Get peaks intersecting with scan
prepareMethodStore-class	Object to handle all peak detection methods
prepareScans	Preprocess scans
prepareScans-MsData-method	Scan preprocessing in MsData objects
rbindGtable	Replacement for the gtable rbind
scanMode	Get and set the mode of scans in an MsScanList
scanNoise	Get intensity threshold for a given signal-to-noise ratio
scans	Extract scans from an object
scans-MsChromList-method	Extract the scans that make up a chromatogram
scans-MsData-method	Extract scans from an MsData object
scans-MsIonList-method	Extract the scans that make up an ion list
scans-MsPeakList-method	Get scans from peak
uNames	Get unique names of elements