SilacPeptideExperiment-class {pulsedSilac} | R Documentation

## SilacPeptideExperiment class

### 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`

[Package pulsedSilac version 1.9.1 Index]