MSnbase

Representation of chromatographic MS data

Class "FeatComp"

Features of Interest

Container for multiple Chromatogram objects

The "MIAPE" Class for Storing Proteomics Experiment Information

Class MSmap

The 'MSnExp' Class for MS Data And Meta-Data

The "MSnProcess" Class

The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

Storing multiple related MSnSets

MSnbase options

List of Spectrum objects along with annotations

Parse MzTab files

The OnDiskMSnExp Class for MS Data And Meta-Data

Simple processing step class

The "ReporterIons" Class

The "Spectrum" Class

The "Spectrum1" Class for MS1 Spectra

The "Spectrum2" Class for MSn Spectra

TMT 6/10-plex sets

Adds Identification Data

Identify aggregation outliers

Generate an average MSnSet

Bin 'MSnExp' or 'Spectrum' instances

Calculate ions produced by fragmentation.

Extract chromatogram object(s)

Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances

Combines features in an MSnSet object

Combine Spectra

Combine signal from consecutive spectra of LCMS experiments

Keep only common feature names

Compare two MSnSets

Compare Spectra of an 'MSnExp' or 'Spectrum' instances

Combine spectra to a consensus spectrum

MSnbase Deprecated and Defunct

Estimate the m/z resolution of a spectrum

Estimate m/z scattering in consecutive scans

Noise Estimation for 'Spectrum' instances

Extracts precursor-specific spectra from an 'MSnExp' object

Extract data from MSnbase objects for use in Spectra

Expand or merge feature variables

Converts factors to strings

Calculates coeffivient of variation for features

Fills up a vector

Filter out unreliable PSMs.

Format Retention Time

Amino acids

Atomic mass.

Return a variable name

Returns the matching column names of indices.

Checks if raw data files have any spectra or chromatograms

iPQF: iTRAQ (and TMT) Protein Quantification based on Features

iTRAQ 4-plex set

NA heatmap visualisation for 2 groups

Quantitative proteomics data imputation

Get mode from mzML data file

Example MSnExp and MSnSet data sets

Tests equality of list elements class

Convert to camel case by replacing dots by captial letters

Create a data with missing values

Combine a list of spectra to a single spectrum

Documenting missing data visualisation

Coerce identification data to a data.frame

How many features in a group?

Count the number of quantitfied features.

Overview of missing value

Navigate an MSnExp object

Combine peptides into proteins.

Normalisation of MSnExp, MSnSet and Spectrum objects

Non-parametric coefficient of variation

Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

Peak Detection for 'MSnExp' or 'Spectrum' instances

Plotting 'MSnExp' and 'Spectrum' object(s)

The 'plot2d' method for 'MSnExp' quality assessment

The 'plotDensity' method for 'MSnExp' quality assessment

The delta m/z plot

Exploring missing data in 'MSnSet' instances

Plotting a 'Spectrum' vs another 'Spectrum' object.

Number of precursor selection events

Performs reporter ions purity correction

Quantifies 'MSnExp' and 'Spectrum' objects

Imports mass-spectrometry raw data files as 'MSnExp' instances.

Read 'MSnSet'

Import mgf files as 'MSnExp' instances.

Import peptide-spectrum matches

Read an 'mzTab' file

Read an 'mzTab' file

Read SRM/MRM chromatographic data

Reduce a data.frame

Removes non-identified features

Removes low intensity peaks

Removes reporter ion tag peaks

Select feature variables of interest

Smooths 'MSnExp' or 'Spectrum' instances

Trims 'MSnExp' or 'Spectrum' instances

Update MSnbase objects

Write MS data to mzML or mzXML files

Write an experiment or spectrum to an mgf file

Export an MzTab object as mzTab file.