SilacPeptideExperiment-class: SilacPeptideExperiment 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 peptide level data. The metadata slot comes already initialized with the metaoptions (see details).

Details

The SilacPeptideExperiment class has been designed to store peptide 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 SilacProteinExperiment and SilacProteomicsExperiment classes.

ProteinExperiment 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.

proteinCol

character indicating the column name of rowData(x) that defines to which protein a peptide is assigned.

Constructor

See SilacPeptideExperiment-constructor for details.

Accessors

See SilacProteinPeptideExperiment-accessors for details.

See Also

SilacPeptideExperiment-constructor, SilacProteinPeptideExperiment-accessors, SummarizedExperiment

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