SilacProteinExperiment-class: SilacProteinExperiment class

In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description

S4 class that extends the SummarizedExperiment class. This class is designed for proteomics data, more especifically protein level data. The metadata slot comes already initialized with the metaoptions (see details).

Details

The SilacProteinExperiment class has been designed to store protein level data and to be used in the functions provided in this package for pulsed SILAC data analysis; in combination with the other two classes from the package: the SilacPeptideExperiment and SilacProteomicsExperiment classes.

SilacProteinExperiment metaoptions are stored in the metadata slot This contains a list with some parameters that are automatically initialized by the constructor. Some parameters are mandatory for certain functions or operations. The user can add or remove items at their discretion. These parameters are meant to help automate certain pipeline or data analysis steps. These metaoptions are:

conditionCol

character indicating the column name of colData(x) that defines the different experiment conditions.

timeCol

character indicating the column name of colData(x) that defines the different timepoints of the experiment.

Constructor

See SilacProteinExperiment-constructor for details.

Accessors

See SilacProteinPeptideExperiment-accessors for details.

See Also

SilacProteinExperiment-constructor, SilacProteinPeptideExperiment-accessors, SummarizedExperiment

pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.