GOComparisonHelpfile

Description

GOComparison is a function which takes as input an object of class GOsets, containing the results of a GO enrichment analysis applied to both levels, and returns an object of class GOsims, containing a variety of comparisons among the enriched GO terms.

Usage

GOComparison(object)

Arguments

Value

An object of class GOsims

Author(s)

Toma Tebaldi, Erik Dassi, Galena Kostoska

References

Wang et al.(2007) A new method to measure the semantic similarity of go terms Bioinformatics , 23:0 1274-81, May 2007.

See Also

GOEnrichment GOsets GOsims

Examples

data(tRanslatomeSampleData)
GOComparison(CCEnrichment)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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/GOComparison.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOComparison
> ### Title: GOComparisonHelpfile
> ### Aliases: GOComparison
> ### Keywords: DEGs GO enrichment analysis Fisher test
> 
> ### ** Examples
> 
> data(tRanslatomeSampleData)
> GOComparison(CCEnrichment)
  ontology level         GO.ID       
4 "CC"     "both levels" "GO:0005759"
2 "CC"     "both levels" "GO:0042627"
1 "CC"     "both levels" "GO:0034361"
3 "CC"     "both levels" "GO:0034366"
  term                                         
4 "mitochondrial matrix"                       
2 "chylomicron"                                
1 "very-low-density lipoprotein particle"      
3 "spherical high-density lipoprotein parti..."
     ontology direction                        start.GO.ID 
[1,] "CC"     "transcriptome  to  translatome" "GO:0005759"
[2,] "CC"     "transcriptome  to  translatome" "GO:0042627"
[3,] "CC"     "transcriptome  to  translatome" "GO:0034361"
[4,] "CC"     "transcriptome  to  translatome" "GO:0034366"
[5,] "CC"     "translatome  to  transcriptome" "GO:0005759"
[6,] "CC"     "translatome  to  transcriptome" "GO:0042627"
     start.term                                    end.GO.ID   
[1,] "mitochondrial matrix"                        "GO:0005759"
[2,] "chylomicron"                                 "GO:0042627"
[3,] "very-low-density lipoprotein particle"       "GO:0034361"
[4,] "spherical high-density lipoprotein parti..." "GO:0034366"
[5,] "mitochondrial matrix"                        "GO:0005759"
[6,] "chylomicron"                                 "GO:0042627"
     end.term                                      similarity.score
[1,] "mitochondrial matrix"                        "1"             
[2,] "chylomicron"                                 "1"             
[3,] "very-low-density lipoprotein particle"       "1"             
[4,] "spherical high-density lipoprotein parti..." "1"             
[5,] "mitochondrial matrix"                        "1"             
[6,] "chylomicron"                                 "1"             
CC 
 1 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>