Transcriptogram-class {transcriptogramer} | R Documentation

## Class Transcriptogram

### Description

This S4 class includes methods to use expression values with ordered proteins.

### Slots

`association`

  A data.frame containing two columns, with rows containing ENSEMBL Peptide IDs that are connected.

`ordering`

  A data.frame containing two columns, the first one with ENSEMBL Peptide IDs, and the second containing its respective position.

`transcriptogramS1`

  A data.frame produced as the result of averaging over all identifiers related to the same protein.

`transcriptogramS2`

  A data.frame produced as the result of averaging over the window.

`radius`

  An non-negative integer referring to the window radius.

`status`

  An integer used internally to check the status of the object.

`DE`

  A data.frame of differentially expressed proteins.

`clusters`

  A list indicating the first and the last position belonging to each cluster.

`pbc`

  Logical value used internally to indicate the overlapping of the first and the last cluster.

`Protein2Symbol`

  A data.frame containing two columns, the first one with ENSEMBL Peptide IDs, and the second containing its respective Symbol.

`Protein2GO`

  A data.frame containing two columns, the first one with ENSEMBL Peptide IDs, and the second containing its respective Gene Ontology accession.

`Terms`

  A data.frame containing the enriched Gene Ontology terms.

`genesInTerm`

  A list of GO terms and its respective ENSEMBL Peptide IDs, feeded by the clusterEnrichment() method.

### Author(s)

Diego Morais

### See Also

transcriptogramPreprocess, DE, radius, orderingProperties, connectivityProperties, transcriptogramStep1, transcriptogramStep2, differentiallyExpressed, clusterVisualization, clusterEnrichment, enrichmentPlot

[Package transcriptogramer version 1.12.0 Index]