Last data update: 2014.03.03

 R: Class 'GOsets'
GOsets-classR Documentation

Class GOsets

Description

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.

Slots

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:

  1. ontology, GO ontology of the term, either BP,CC or MF.

  2. 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.

  3. GO.ID, Gene Ontology accession ID of the term.

  4. term, Gene Ontology name of the term.

  5. annotated, number of genes in the human genome associated to the GO term.

  6. significant, number of genes in the list of DEGs associated to the GO term.

  7. expected, number of genes in the list of DEGs expected to be associated to the GO term by chance.

  8. expected, number of genes in the list of DEGs expected to be associated to the GO term by chance.

  9. 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).

  10. 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.

Accessors

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.

Methods

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.

Author(s)

Toma Tebaldi, Erik Dassi, Galena Kostoska

References

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.

See Also

EnrichedSets GOComparison DEGs

Examples

showClass("GOsets")

Results


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> library(tRanslatome)
Loading required package: limma
Loading required package: sigPathway
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq
Loading required package: BiocGenerics
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Attaching package: 'BiocGenerics'

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    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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    anyMissing, rowMedians

Loading required package: locfit
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    Welcome to 'DESeq'. For improved performance, usability and
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Attaching package: 'S4Vectors'

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    colMeans, colSums, expand.grid, rowMeans, rowSums


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    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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Loading required package: org.Hs.eg.db

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Attaching package: 'gplots'

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Loading required package: plotrix

Attaching package: 'plotrix'

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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/GOsets.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOsets-class
> ### Title: Class 'GOsets'
> ### Aliases: GOsets-class Radar,GOsets-method Heatmap,GOsets-method
> ###   GOComparison,GOsets-method show,GOsets-method
> ### Keywords: classes GO enrichment analysis
> 
> ### ** Examples
> 
> showClass("GOsets")
Class "GOsets" [package "tRanslatome"]

Slots:
                                                
Name:        enriched.table label.level.enriched
Class:           data.frame            character

Extends: "EnrichedSets"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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