SilacProteomicsExperiment-class: SilacProteomicsExperiment class
In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description Details Slots Constructor Accessors See Also

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.

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.

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.