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xcms (version 1.46.0)

LC/MS and GC/MS Data Analysis

Description

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

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Version

Version

1.46.0

License

GPL (>= 2) + file LICENSE

Issues

Pull Requests

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Repository

http://metlin.scripps.edu/download/ and https://github.com/sneumann/xcms

Maintainer

Steffen Neumann

Last Published

February 15th, 2017

Functions in xcms (1.46.0)

calibrate-methods

Calibrate peaks for correcting unprecise m/z values

AutoLockMass-methods

Automatic parameter for Lock mass fixing AutoLockMass ~~

Combine xcmsSet objects

Determine which peaks are absent / present in a sample class

Find row and column maximum values

collect-methods

Collect MS^n peaks into xcmsFragments

Allocate double, integer, or logical matricies

Find start and end points of a peak

diffreport-methods

Create report of analyte differences

Empirically Transformed Gaussian function

findEqualGreater

Find values in sorted vectors

Find fragment ions in xcmsFragment objects

findPeaks.massifquant-methods

Feature detection for XC-MS data.

findPeaks.centWave-methods

Feature detection for high resolution LC/MS data

fillPeaks.MSW-methods

Integrate areas of missing peaks in FTICR-MS data

Find neutral losses in xcmsFragment objects

Apply an convolution filter using an FFT

findPeaks-methods

Feature detection for GC/MS and LC/MS Data - methods

fillPeaks-methods

Integrate areas of missing peaks

fillPeaks.chrom-methods

Integrate areas of missing peaks

peakTable-methods

Create report of aligned peak intensities

Plot extracted ion chromatograms from multiple files

profRange-methods

Specify a subset of profile mode data

profMethod-methods

Get and set method for generating profile data

Get a raw data matrix

Determine a subset of rectangles with unique, non-overlapping areas

specDist.cosine

a Distance function based on matching peaks

findPeaks.MS1-methods

Collecting MS1 precursor peaks

findPeaks.matchedFilter-methods

Feature detection in the chromatographic time domain

groupnames-methods

Generate unque names for peak groups

groupval-methods

Extract a matrix of peak values for each group

Correlation coefficient panel for pairs function

peakPlots-methods

Plot a grid of a large number of peaks

Plot retention time deviation profiles

plotRaw-methods

Scatterplot of raw data points

Set retention time window to a specified width

retcor.peakgroups-methods

Align retention times across samples

Group peaks from different samples together

Group Peaks via High Resolution Alignment

Group peaks from different samples together

Group peaks from different samples together

Correct retention time from different samples

Align retention times across samples with Obiwarp

getPeaks-methods

Get peak intensities for specified regions

Divide an xcmsSet object

Copy MSn data in an xcmsRaw to the MS slots

getScan-methods

Get m/z and intensity values for a single mass scan

Fill in NA values at the extremes of a vector

netCdfSource-class

Class "netCdfSource", for reading raw data from netCDF files

High-performance, low-level access to NetCDF data files

specDist.meanMZmatch

a Distance function based on matching peaks

Correct gaps in data

verify.mzQuantM

Verify an mzQuantML file

Constructor for xcmsFragments objects which holds Tandem MS peaks

Constructor for xcmsRaw objects which reads NetCDF/mzXML files

xcmsPeaks-class

A matrix of peaks

getSpec-methods

Get average m/z and intensity values for multiple mass scans

Plot log intensity image of a xcmsRaw object

getXcmsRaw-methods

Load the raw data for one or more files in the xcmsSet

levelplot-methods

Plot log intensity image of a xcmsRaw object

Plot m/z and RT deviations for QC purposes without external reference data

plotPeaks-methods

Plot a grid of a large number of peaks

profMedFilt-methods

Median filtering of the profile matrix

Generation of profile data

profStep-methods

Get and set m/z step for generating profile data

Generate p-values for a vector of t-statistics

write.cdf-methods

Save an xcmsRaw object to file

write.mzdata-methods

Save an xcmsRaw object to a file

sampnames-methods

Get sample names

specDist-methods

Distance methods for xcmsSet, xcmsRaw and xsAnnotate

write.mzQuantML-methods

Save an xcmsSet object to an PSI mzQuantML file

Class xcmsEIC, a class for multi-sample extracted ion chromatograms

findPeaks.MSW-methods

Feature detection for single-spectrum non-chromatography MS data

Get extracted ion chromatograms for specified m/z ranges

loadRaw-methods

Read binary data from a source

Apply a median filter to a matrix

plotEIC-methods

Plot extracted ion chromatograms for specified m/z range

plotChrom-methods

Plot extracted ion chromatograms from the profile matrix

plotTIC-methods

Plot total ion count

plotSurf-methods

Plot profile matrix 3D surface using OpenGL

Get extracted ion chromatograms for specified m/z range

rampSource-class

Class "rampSource", for reading raw data from netCDF files

specDist.peakCount-methods

a Distance function based on matching peaks

Calculate noise for a sparse continuum mass spectrum

Class xcmsSet, a class for preprocessing peak data

Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files

plotScan-methods

Plot a single mass scan

plotSpec-methods

Plot mass spectra from the profile matrix

Identify peaks in a sparse continuum mode spectrum

Divide an xcmsRaw object

xcmsFileSource-class

Base class for loading raw data from a file

xcmsFragments-class

Class xcmsFragments, a class for handling Tandem MS and MS$^n$ data

xcmsSource-class

Virtual class for raw data sources

xcmsSource-methods

Create an xcmsSource object in a flexible way