Allocate double, integer, or logical matricies
Empirically Transformed Gaussian function
findPeaks.centWave-methods
Feature detection for high resolution LC/MS data
findPeaks.massifquant-methods
Feature detection for XC-MS data.
Get extracted ion chromatograms for specified m/z ranges
Feature detection for single-spectrum non-chromatography MS data
Read binary data from a source
Create report of analyte differences
Find start and end points of a peak
Feature detection for GC/MS and LC/MS Data - methods
Find neutral losses in xcmsFragment objects
Collecting MS1 precursor peaks
Plot log intensity image of a xcmsRaw object
findPeaks.matchedFilter-methods
Feature detection in the chromatographic time domain
Integrate areas of missing peaks
Integrate areas of missing peaks
Fill in NA values at the extremes of a vector
Copy MSn data in an xcmsRaw to the MS slots
Plot extracted ion chromatograms from the profile matrix
Get and set method for generating profile data
Plot extracted ion chromatograms for specified m/z range
Specify a subset of profile mode data
Determine which peaks are absent / present in a sample class
Automatic parameter for Lock mass fixing AutoLockMass ~~
Find values in sorted vectors
Find fragment ions in xcmsFragment objects
Load the raw data for one or more files in the xcmsSet
Get average m/z and intensity values for multiple mass scans
Apply a median filter to a matrix
Correlation coefficient panel for pairs function
High-performance, low-level access to NetCDF data files
Plot a grid of a large number of peaks
Generation of profile data
Median filtering of the profile matrix
a Distance function based on matching peaks
Class "netCdfSource", for reading raw data from
netCDF files
Scatterplot of raw data points
Correct retention time from different samples
Align retention times across samples with Obiwarp
Plot retention time deviation profiles
Save an xcmsRaw object to file
Calibrate peaks for correcting unprecise m/z values
Combine xcmsSet objects
Apply an convolution filter using an FFT
Integrate areas of missing peaks in FTICR-MS data
Get peak intensities for specified regions
Save an xcmsRaw object to a file
Get m/z and intensity values for a single mass scan
A matrix of peaks
Constructor for xcmsRaw objects which reads NetCDF/mzXML files
Group Peaks via High Resolution Alignment
Group peaks from different samples together
Plot a grid of a large number of peaks
Plot m/z and RT deviations for QC purposes without external reference data
Plot a single mass scan
Plot mass spectra from the profile matrix
Collect MS^n peaks into xcmsFragments
Find row and column maximum values
Group peaks from different samples together
Group peaks from different samples together
Generate unque names for peak groups
Plot log intensity image of a xcmsRaw object
Plot profile matrix 3D surface using OpenGL
Plot total ion count
retcor.peakgroups-methods
Align retention times across samples
Set retention time window to a specified width
Divide an xcmsRaw object
Identify peaks in a sparse continuum mode spectrum
Save an xcmsSet object to an PSI mzQuantML file
Get a raw data matrix
Determine a subset of rectangles with unique, non-overlapping areas
specDist.peakCount-methods
a Distance function based on matching peaks
Calculate noise for a sparse continuum mass spectrum
Correct gaps in data
Verify an mzQuantML file
Get extracted ion chromatograms for specified m/z range
Class "rampSource", for reading raw data from
netCDF files
Divide an xcmsSet object
Gaussian Model
Base class for loading raw data from a file
Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data
a Distance function based on matching peaks
Class xcmsSet, a class for preprocessing peak data
Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files
Extract a matrix of peak values for each group
Plot extracted ion chromatograms from multiple files
Create report of aligned peak intensities
Get and set m/z step for generating profile data
Generate p-values for a vector of t-statistics
Get sample names
Class xcmsEIC, a class for multi-sample extracted ion chromatograms
Distance methods for xcmsSet, xcmsRaw and xsAnnotate
Constructor for xcmsFragments objects which holds Tandem MS
peaks
xcmsPapply
Create an xcmsSource object in a flexible way
Virtual class for raw data sources