A class generated from the function GOComparison() containing the result of the differential expression analysis at the two expression levels.
Slots
similarity.matrix:
Object of class matrix containing the semantic similarity comparison between the GO terms enriched at the two levels of analysis. The matrix contains one row for each pairwise comparison between GO terms enriched in the two levels, while columns are organized as follows:
direction, direction of the comparison: "first level to second level" means that an enriched GO term from the first level is compared to the most similar GO term enriched in the second level, "second level to first level" means that an enriched GO term from the second level is compared to the most similar GO term enriched in the first level. Level names are taken from the object of class GOsets given as input to the function GOcomparison.
ontology, GO ontology of the two terms, either BP,CC or MF.
level, gene expression levels for which the term is enriched, either "first level only", "second level only" or "both levels". Level names are taken from the object of class GOsets given as input to the function GOcomparison.
start.GO.ID, Gene Ontology accession ID of the first term of the comparison.
start.term, Gene Ontology name of the first term of the comparison.
end.GO.ID, Gene Ontology accession ID of the second term of the comparison.
end.term, Gene Ontology name of the second term of the comparison.
similarity.score, semantic similarity value between the two campared GO terms.
identity.matrix:
Object of class matrix containing the identity comparison between the GO terms enriched at the two levels of analysis. The matrix 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, gene expression levels for which the term is enriched, either "first level only", "second level only" or "both levels". Level names are taken from the object of class GOsets given as input to the function GOcomparison.
GO.ID, Gene Ontology accession ID of the term.
term, Gene Ontology name of the term.
average.similarity.scores:
Object of class vector containing the general semantic similarity scores between the GO terms enriched at the two levels of analysis. One similarity score, ranging from 0 to 1, is produced for each GO ontology having at least one enriched term.
Accessors
identity.matrix
signature(object = "GOsims"): displays the slot identity.matrix.
similarity.matrix
signature(object = "GOsims"): displays the slot similarity.matrix.
average.similarity.scores
signature(object = "GOsims"): displays the slot average.similarity.scores.
Methods
IdentityPlot
signature(object = "GOsims"): enables the generation of a barplot where, for each GO ontology, the number of GO terms enriched at different levels are displayed.
SimilarityPlot
signature(object = "GOsims"): enables the generation of a barplot where, for each GO ontology, the semantic similarity value between GO terms enriched at different levels is displayed.
Author(s)
Toma Tebaldi, Erik Dassi, Galena Kostoska
See Also
TranslatomeDatasetcomputeDEGsGOEnrichmentGOsets
Examples
showClass("GOsims")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
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'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Loading required package: lattice
Welcome to 'DESeq'. For improved performance, usability and
functionality, please consider migrating to 'DESeq2'.
Loading required package: edgeR
Loading required package: RankProd
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: org.Hs.eg.db
Loading required package: GOSemSim
Loading required package: Heatplus
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: plotrix
Attaching package: 'plotrix'
The following object is masked from 'package:gplots':
plotCI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/GOsims.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOsims-class
> ### Title: Class 'GOsims'
> ### Aliases: GOsims-class identity.matrix,GOsims-method
> ### similarity.matrix,GOsims-method
> ### average.similarity.scores,GOsims-method IdentityPlot,GOsims-method
> ### SimilarityPlot,GOsims-method
> ### Keywords: classes GO enrichment analysis
>
> ### ** Examples
>
> showClass("GOsims")
Class "GOsims" [package "tRanslatome"]
Slots:
Name: similarity.matrix identity.matrix
Class: matrix matrix
Name: average.similarity.scores
Class: vector
>
>
>
>
>
> dev.off()
null device
1
>
providing 
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