Transcriptogram-class {transcriptogramer} | R Documentation |
This S4 class includes methods to use expression values with ordered proteins.
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.
Diego Morais
transcriptogramPreprocess, DE, radius, orderingProperties, connectivityProperties, transcriptogramStep1, transcriptogramStep2, differentiallyExpressed, clusterVisualization, clusterEnrichment, enrichmentPlot