Transcriptogram-class: Class Transcriptogram

In transcriptogramer: Transcriptional analysis based on transcriptograms

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

transcriptogramer documentation built on Nov. 8, 2020, 8:17 p.m.