# Tools for high-throughput metabolomics

## Documentation for package ‘yamss’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

bakedpi | Process raw data to compute density estimate.
CMSproc-class | A class to hold chromatography-mass spectrometry preprocessing information.
CMSraw-class | A class to hold chromatography-mass spectrometry raw data and metadata.
cmsRawExample | An example cmsRaw object
CMSslice | A class to hold chromatography-mass spectrometry peak bounds and quantifications.
CMSslice-class | A class to hold chromatography-mass spectrometry peak bounds and quantifications.
colData-method | A class to hold chromatography-mass spectrometry raw data and metadata.
densityCutoff | A class to hold chromatography-mass spectrometry peak bounds and quantifications.
densityEstimate | A class to hold chromatography-mass spectrometry preprocessing information.
densityQuantiles | A class to hold chromatography-mass spectrometry preprocessing information.
diffrep | Perform differential analysis.
getEICS | Compute extracted ion chromatograms for multiple regions.
getTIC | Compute total ion chromatogram (TIC) for a sample.
peakBounds | A class to hold chromatography-mass spectrometry peak bounds and quantifications.
peakQuants | A class to hold chromatography-mass spectrometry peak bounds and quantifications.
plotDensityRegion | Image plot of region of density estimate.
readMSdata | Read raw mass spectral data files.
show-method | A class to hold chromatography-mass spectrometry preprocessing information.
show-method | A class to hold chromatography-mass spectrometry raw data and metadata.
show-method | A class to hold chromatography-mass spectrometry peak bounds and quantifications.
slicepi | Process raw data to compute density estimate.