SilacProteomicsExperiment-class {pulsedSilac} | R Documentation

## SilacProteomicsExperiment class

### Description

S4 class that contains a `SilacProteinExperiment` object and a `SilacPeptideExperiment` object. The two objects are linked by a `data.frame` (linkerDf). This class can be used to manage both protein and peptide data at the same time.

### Details

The `SilacProteomicsExperiment` object is just a `SilacProteinExperiment` object and a `SilacPeptideExperiment` object together.

The rows of the `SilacProteinExperiment` object represent proteins. The rows of the `SilacPeptideExperiment` object represent peptides.

The columns of the `SilacProteomicsExperiment` object represent samples. Samples are shared at both protein and peptide levels.

Experiment-wide information can be stored in the `metadata` slot, which is accessed with the `metadata` function. This contains a `list` object in which each item is left to the discretion of the user. Some possible examples could be: data of the experiment, author, machine used, etc.

SilacProteomicsExperiment options 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: 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.

idColProt

  A `character` indicating which column from the rowData (protein) should be used as ids.

idColPept

  A `character` indicating which column from the rowData (peptides) should be used as ids.

linkedSubset

  A `logical` if subsetting should be linked between proteins and peptide.

subsetMode

  A `character`, either 'protein' or 'peptide' indicating which level should be used first when subsetting.

### Slots

`SilacProteinExperiment`

  Contains a `SilacProteinExperiment` object.

`SilacPeptideExperiment`

  Contains a `SilacPeptideExperiment` object.

`colData`

  Contains a `data.frame` with sample information like conditions, replicates, etc.

`linkerDf`

  Contains a `data.frame` that has been created with `buildLinkerDf`. It contains the relationships between proteins and peptides.

`metadata`

  Contains a `list` to store any kind of experiment-wide data and the metaoptions.

### Constructor

See SilacProteomicsExperiment-constructor for details.

### Accessors

See SilacProteomicsExperiment-accessors for details.

### See Also

`SilacProteomicsExperiment-constructor`, `SilacProteomicsExperiment-accessors`, `SilacProteinExperiment`, `SilacPeptideExperiment`

[Package pulsedSilac version 1.1.4 Index]