Learn R Programming

xcms (version 1.48.0)

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.

Copy Link

Version

Version

1.48.0

License

GPL (>= 2) + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

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

Maintainer

Steffen Neumann

Last Published

February 15th, 2017

Functions in xcms (1.48.0)

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

findPeaks.MSW-methods

Feature detection for single-spectrum non-chromatography MS data

loadRaw-methods

Read binary data from a source

diffreport-methods

Create report of analyte differences

Find start and end points of a peak

findPeaks-methods

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

Find neutral losses in xcmsFragment objects

findPeaks.MS1-methods

Collecting MS1 precursor peaks

Plot log intensity image of a xcmsRaw object

findPeaks.matchedFilter-methods

Feature detection in the chromatographic time domain

fillPeaks-methods

Integrate areas of missing peaks

fillPeaks.chrom-methods

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

plotChrom-methods

Plot extracted ion chromatograms from the profile matrix

profMethod-methods

Get and set method for generating profile data

plotEIC-methods

Plot extracted ion chromatograms for specified m/z range

profRange-methods

Specify a subset of profile mode data

Determine which peaks are absent / present in a sample class

AutoLockMass-methods

Automatic parameter for Lock mass fixing AutoLockMass ~~

findEqualGreater

Find values in sorted vectors

Find fragment ions in xcmsFragment objects

getXcmsRaw-methods

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

getSpec-methods

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

peakPlots-methods

Plot a grid of a large number of peaks

Generation of profile data

profMedFilt-methods

Median filtering of the profile matrix

specDist.cosine

a Distance function based on matching peaks

netCdfSource-class

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

plotRaw-methods

Scatterplot of raw data points

Correct retention time from different samples

Align retention times across samples with Obiwarp

Plot retention time deviation profiles

write.cdf-methods

Save an xcmsRaw object to file

calibrate-methods

Calibrate peaks for correcting unprecise m/z values

Combine xcmsSet objects

Apply an convolution filter using an FFT

fillPeaks.MSW-methods

Integrate areas of missing peaks in FTICR-MS data

getPeaks-methods

Get peak intensities for specified regions

write.mzdata-methods

Save an xcmsRaw object to a file

getScan-methods

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

xcmsPeaks-class

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

plotPeaks-methods

Plot a grid of a large number of peaks

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

plotScan-methods

Plot a single mass scan

plotSpec-methods

Plot mass spectra from the profile matrix

collect-methods

Collect MS^n peaks into xcmsFragments

Find row and column maximum values

Group peaks from different samples together

Group peaks from different samples together

groupnames-methods

Generate unque names for peak groups

levelplot-methods

Plot log intensity image of a xcmsRaw object

plotSurf-methods

Plot profile matrix 3D surface using OpenGL

plotTIC-methods

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

write.mzQuantML-methods

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.mzQuantM

Verify an mzQuantML file

Get extracted ion chromatograms for specified m/z range

rampSource-class

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

Divide an xcmsSet 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

specDist.meanMZmatch

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

groupval-methods

Extract a matrix of peak values for each group

Plot extracted ion chromatograms from multiple files

peakTable-methods

Create report of aligned peak intensities

profStep-methods

Get and set m/z step for generating profile data

Generate p-values for a vector of t-statistics

sampnames-methods

Get sample names

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

specDist-methods

Distance methods for xcmsSet, xcmsRaw and xsAnnotate

Constructor for xcmsFragments objects which holds Tandem MS peaks

xcmsSource-methods

Create an xcmsSource object in a flexible way

xcmsSource-class

Virtual class for raw data sources