GOsets: Class 'GOsets'
In tRanslatome: Comparison between multiple levels of gene expression

Description Slots Accessors Methods Author(s) References See Also Examples

A class generated from the function GOEnrichment() containing the overrepresented Gene Ontology terms from the lists of differentially expressed genes coming from the analysis of two different expression levels.

enriched.table:

Object of class data.frame containing all the GO enrichment analysis. The data frame contains one row for each GO term, while columns are organized as follows:

ontology, GO ontology of the term, either BP,CC or MF.
level, level of analysis on which the enrichment is calculated. The names of the two levels are taken from the object DEGs given as an input to the function GOEnrichment.
GO.ID, Gene Ontology accession ID of the term.
term, Gene Ontology name of the term.
annotated, number of genes in the human genome associated to the GO term.
significant, number of genes in the list of DEGs associated to the GO term.
expected, number of genes in the list of DEGs expected to be associated to the GO term by chance.
expected, number of genes in the list of DEGs expected to be associated to the GO term by chance.
pv.fisher, enrichment p-value calculated with the Fisher test. The result is dependent on the method chosen to calculate enrichment(classic,elim, weight,weight01 or parentchild).
pv.fisher.BH, the Benjamini-Hochberg corrected enrichment p-value calculated with the Fisher test according to the chosen enrichment method.

label.level.enriched:

Object of class character specifying the names of the two levels compared in the experiment.

enriched.table: signature(object = "GOsets"): displays the slot enriched.table.
label.level.enriched: signature(object = "GOsets"): displays the slot label.level.enriched, slot of class character specifying the names of the two levels compared in the experiment.

GOComparison: signature(object = "GOsets"): returns an object of class GOsims, containing identity and semantic similarity comparisons among the enriched GO terms.
Heatmap: signature(object = "GOsets"): enables the generation of a heatmap of the top enriched GO terms for the first and second level of analysis.
Radar: signature(object = "GOsets"): enables the generation of a radar plot of the top enriched GO terms for the first and second level of analysis.
show: signature(object = "GOsets"): displays all the two slots of the class.

Toma Tebaldi, Erik Dassi, Galena Kostoska

Ashburner M et al(2000). Gene ontology: tool for the unification of biology. Nat. Genet. May 2000;25(1):25-9.

Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating go graph structure. Bioinformatics 2006, 22(13):1600-7.

EnrichedSets GOComparison DEGs