The "MSnProcess" Class
NAnnotatedDataFrame-class
Class Containing Measured Variables and Their Meta-Data
Description for Multiplexed Experiments.
Bin 'MSnExp' or 'Spectrum' instances
Features of Interest
Parse MzTab
files
Class to Contain Raw Mass-Spectrometry Assays and Experimental
Metadata
Documenting missing data visualisation
Storing multiple related MSnSets
Generate an average MSnSet
Returns the matching column names of indices.
Smooths 'MSnExp' or 'Spectrum' instances
Combines features in an MSnSet
object
Plots a chromatogram
iPQF: iTRAQ (and TMT) Protein Quantification based on Features
extractPrecSpectra-methods
Extracts precursor-specific spectra from an 'MSnExp' object
The "Spectrum" Class
Count the number of quantitfied features.
Class "FeatComp"
NA heatmap visualisation for 2 groups
Compare Spectra of an 'MSnExp' or 'Spectrum' instances
The "Spectrum2" Class for MSMS Spectra
plot.Spectrum.Spectrum-methods
Plotting a 'Spectrum' vs another 'Spectrum' object.
TMT 6-plex set
The "ReporterIons" Class
Quantitative proteomics data imputation
The delta m/z plot
Overview of missing value
addIdentificationData-methods
Adds Identification Data
Format Retention Time
The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data
Normalisation of MSnExp
, MSnSet
and
Spectrum
objects
Plotting 'Spectrum' object(s)
Removes non-identified features
Non-parametric coefficient of variation
Create a data with missing values
Imports mass-spectrometry raw data files as 'MSnExp' instances.
Read an 'mzTab' file
The 'plot2d' method for 'MSnExp' quality assessment
Read an 'mzTab' file
Import mgf files as 'MSnExp' instances.
Number of precursor selection events
Performs reporter ions purity correction
Select feature variables of interest
The "MIAPE" Class for Storing Proteomics Experiment Information
Keep only common feature names
Compare two MSnSets
Example MSnExp
and MSnSet
data sets
Read 'MSnSet'
Removes reporter ion tag peaks
The 'MSnExp' Class for MS Data And Meta-Data
The "Spectrum1" Class for MS1 Spectra
Cleans 'MSnExp' or 'Spectrum' instances
calculateFragments-methods
Calculate ions produced by fragmentation.
Calculate all ratio pairs
Calculates coeffivient of variation for features
Amino acids
Peak Detection for 'MSnExp' or 'Spectrum' instances
iTRAQ 4-plex set
Removes low intensity peaks
Trims 'MSnExp' or 'Spectrum' instances
Extracted ion chromatograms
Class MSmap
Noise Estimation for 'Spectrum' instances
Exploring missing data in 'MSnSet' instances
Atomic mass.
Write an experiment or spectrum to an mgf file
MSnbase: Base Functions and Classes for MS-based Proteomics
MSnbase Deprecated and Defunct
Fills up a vector
Return a variable name
Tests equality of list elements class
Quantifies 'MSnExp' and 'Spectrum' objects
The 'plotDensity' method for 'MSnExp' quality assessment