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Last data update: 2014.03.03

R: GOEnrichmentHelpfile

GOEnrichment

R Documentation

GOEnrichmentHelpfile

Description

GOEnrichment is a function which, given as input an object of class DEGs, identifies overrepresented GO terms among differentially expressed genes. The analysis can be applied to all the GO ontologies or restricted to GO terms specifically belonging to one ontology: molecular function, cellular component or biological process. Moreover the function can identify enriched GO terms for separate classes of genes of interest: only up-regulated genes, only down-regulated genes or both of them together. The output of the function is an object of class GOsets, containing the results of the enrichment analysis.

Usage

GOEnrichment(object, ontology="all", classOfDEGs="both",
    test.method="classic", test.threshold = 0.05, mult.cor=TRUE)

Arguments

`object`	an object of class `DEGs`
`ontology`	a character string specifying the GO ontology of interest: `CC` for Cellular Component, `BP` for Biological Process, `MF` for Molecular Function or `all` for all the three ontologies. The default is set to `all`.
`classOfDEGs`	a character string specifying the class of genes for which we want to detect enriched GO terms: `up` for considering only up-regulated genes, `down` for considering only down-regulated genes, `both` for considering all DEGs, independently from the direction of their changes. The default is set to `both`.
`test.method`	a character string specifying the statistical method to calculate the enrichment. By default it is set to `classic` (enrichment is measured with the classic Fisher exact test), but it can also be set to `elim`, `weight`, `weight01` or `parentchild`. All these methods are implemented in the `topGO` Bioconductor package
`test.threshold`	a numeric value specifying the significance threshold upon which the GO terms are considered significantly over-represented. By default it is se to `0.05`.
`mult.cor`	a boolean variable specifying whether the significance threshold is applied to the multiple test corrected or to the original p-values obtained from the selected enrichment method. By default it is set to `TRUE`.

Value

An object of class GOsets

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

Examples

data(tRanslatomeSampleData)
GOEnrichment(limma.DEGs,ontology="CC",classOfDEGs="up",
    test.method="classic", test.threshold = 0.05,mult.cor = TRUE)

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/GOEnrichment.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOEnrichment
> ### Title: GOEnrichmentHelpfile
> ### Aliases: GOEnrichment
> ### Keywords: DEGs GO enrichment analysis
> 
> ### ** Examples
> 
> data(tRanslatomeSampleData)
> GOEnrichment(limma.DEGs,ontology="CC",classOfDEGs="up",
+     test.method="classic", test.threshold = 0.05,mult.cor = TRUE)
 Factor w/ 2 levels "0","1": 1 2 1 1 1 1 1 1 1 1 ...
 - attr(*, "names")= chr [1:17839] "A1BG" "A1CF" "A2M" "A2ML1" ...

Building most specific GOs .....
	( 1480 GO terms found. )

Build GO DAG topology ..........
	( 1747 GO terms and 3424 relations. )

Annotating nodes ...............
	( 17839 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 186 nontrivial nodes
		 parameters: 
			 test statistic: fisher
 Factor w/ 2 levels "0","1": 1 2 1 1 1 1 1 1 1 1 ...
 - attr(*, "names")= chr [1:17839] "A1BG" "A1CF" "A2M" "A2ML1" ...

Building most specific GOs .....
	( 1480 GO terms found. )

Build GO DAG topology ..........
	( 1747 GO terms and 3424 relations. )

Annotating nodes ...............
	( 17839 genes annotated to the GO terms. )

			 -- Classic Algorithm -- 

		 the algorithm is scoring 182 nontrivial nodes
		 parameters: 
			 test statistic: fisher
    ontology level           GO.ID        term                               
18  "CC"     "transcriptome" "GO:0005576" "extracellular region"             
19  "CC"     "transcriptome" "GO:0044444" "cytoplasmic part"                 
20  "CC"     "transcriptome" "GO:0005622" "intracellular"                    
21  "CC"     "transcriptome" "GO:0071682" "endocytic vesicle lumen"          
22  "CC"     "transcriptome" "GO:0060205" "cytoplasmic membrane-bounded v..."
23  "CC"     "transcriptome" "GO:0031983" "vesicle lumen"                    
24  "CC"     "transcriptome" "GO:0005759" "mitochondrial matrix"             
25  "CC"     "transcriptome" "GO:0005737" "cytoplasm"                        
7   "CC"     "transcriptome" "GO:0034364" "high-density lipoprotein parti..."
9   "CC"     "transcriptome" "GO:0005615" "extracellular space"              
8   "CC"     "transcriptome" "GO:0072562" "blood microparticle"              
15  "CC"     "transcriptome" "GO:0031988" "membrane-bounded vesicle"         
16  "CC"     "transcriptome" "GO:0031982" "vesicle"                          
10  "CC"     "transcriptome" "GO:0065010" "extracellular membrane-bounded..."
11  "CC"     "transcriptome" "GO:0070062" "extracellular exosome"            
12  "CC"     "transcriptome" "GO:0043230" "extracellular organelle"          
13  "CC"     "transcriptome" "GO:1903561" "extracellular vesicle"            
5   "CC"     "transcriptome" "GO:0034361" "very-low-density lipoprotein p..."
6   "CC"     "transcriptome" "GO:0034385" "triglyceride-rich lipoprotein ..."
1   "CC"     "transcriptome" "GO:0042627" "chylomicron"                      
2   "CC"     "transcriptome" "GO:0034358" "plasma lipoprotein particle"      
3   "CC"     "transcriptome" "GO:1990777" "lipoprotein particle"             
4   "CC"     "transcriptome" "GO:0032994" "protein-lipid complex"            
17  "CC"     "transcriptome" "GO:0034366" "spherical high-density lipopro..."
14  "CC"     "transcriptome" "GO:0044421" "extracellular region part"        
151 "CC"     "translatome"   "GO:0044421" "extracellular region part"        
161 "CC"     "translatome"   "GO:0031988" "membrane-bounded vesicle"         
171 "CC"     "translatome"   "GO:0031982" "vesicle"                          
181 "CC"     "translatome"   "GO:0005622" "intracellular"                    
191 "CC"     "translatome"   "GO:0005759" "mitochondrial matrix"             
201 "CC"     "translatome"   "GO:0005576" "extracellular region"             
211 "CC"     "translatome"   "GO:0005737" "cytoplasm"                        
51  "CC"     "translatome"   "GO:0065010" "extracellular membrane-bounded..."
61  "CC"     "translatome"   "GO:0070062" "extracellular exosome"            
71  "CC"     "translatome"   "GO:0034364" "high-density lipoprotein parti..."
81  "CC"     "translatome"   "GO:0043230" "extracellular organelle"          
91  "CC"     "translatome"   "GO:1903561" "extracellular vesicle"            
26  "CC"     "translatome"   "GO:0042627" "chylomicron"                      
110 "CC"     "translatome"   "GO:0072562" "blood microparticle"              
101 "CC"     "translatome"   "GO:0034358" "plasma lipoprotein particle"      
111 "CC"     "translatome"   "GO:1990777" "lipoprotein particle"             
121 "CC"     "translatome"   "GO:0032994" "protein-lipid complex"            
131 "CC"     "translatome"   "GO:0005615" "extracellular space"              
31  "CC"     "translatome"   "GO:0034361" "very-low-density lipoprotein p..."
41  "CC"     "translatome"   "GO:0034385" "triglyceride-rich lipoprotein ..."
141 "CC"     "translatome"   "GO:0034366" "spherical high-density lipopro..."
    annotated significant expected pv.fisher pv.fisher.BH  
18  " 4505"   "18"        " 7.83"  "0.00010" "5.822222e-03"
19  " 7897"   "24"        "13.72"  "0.00018" "9.928421e-03"
20  "13838"   "31"        "24.05"  "0.00038" "1.905455e-02"
21  "   17"   " 2"        " 0.03"  "0.00039" "1.905455e-02"
22  "   83"   " 3"        " 0.14"  "0.00040" "1.905455e-02"
23  "   85"   " 3"        " 0.15"  "0.00043" "1.959304e-02"
24  "  404"   " 5"        " 0.70"  "0.00061" "2.663667e-02"
25  "10474"   "27"        "18.20"  "0.00064" "2.682880e-02"
7   "   26"   " 4"        " 0.05"  "1.1e-07" "1.646857e-05"
9   " 1361"   "12"        " 2.37"  "1.3e-06" "1.513778e-04"
8   "  143"   " 6"        " 0.25"  "1.5e-07" "1.965000e-05"
15  " 3545"   "17"        " 6.16"  "1.7e-05" "1.187733e-03"
16  " 3669"   "17"        " 6.38"  "2.7e-05" "1.768500e-03"
10  " 2769"   "16"        " 4.81"  "3.2e-06" "2.740923e-04"
11  " 2769"   "16"        " 4.81"  "3.2e-06" "2.740923e-04"
12  " 2782"   "16"        " 4.83"  "3.4e-06" "2.740923e-04"
13  " 2782"   "16"        " 4.83"  "3.4e-06" "2.740923e-04"
5   "   20"   " 4"        " 0.03"  "3.5e-08" "6.113333e-06"
6   "   20"   " 4"        " 0.03"  "3.5e-08" "6.113333e-06"
1   "   13"   " 4"        " 0.02"  "5.3e-09" "1.860200e-06"
2   "   38"   " 5"        " 0.07"  "5.4e-09" "1.860200e-06"
3   "   38"   " 5"        " 0.07"  "5.4e-09" "1.860200e-06"
4   "   40"   " 5"        " 0.07"  "7.1e-09" "1.860200e-06"
17  "    8"   " 2"        " 0.01"  "8.1e-05" "4.993412e-03"
14  " 3777"   "18"        " 6.56"  "8.2e-06" "6.138286e-04"
151 " 3777"   "16"        " 6.35"  "0.00011" "7.685333e-03"
161 " 3545"   "15"        " 5.96"  "0.00021" "1.375500e-02"
171 " 3669"   "15"        " 6.17"  "0.00032" "1.972706e-02"
181 "13838"   "30"        "23.27"  "0.00049" "2.852889e-02"
191 "  404"   " 5"        " 0.68"  "0.00052" "2.868211e-02"
201 " 4505"   "16"        " 7.58"  "0.00091" "4.768400e-02"
211 "10474"   "26"        "17.61"  "0.00096" "4.790857e-02"
51  " 2769"   "15"        " 4.66"  "1.1e-05" "1.280889e-03"
61  " 2769"   "15"        " 4.66"  "1.1e-05" "1.280889e-03"
71  "   26"   " 3"        " 0.04"  "1.1e-05" "1.280889e-03"
81  " 2782"   "15"        " 4.68"  "1.1e-05" "1.280889e-03"
91  " 2782"   "15"        " 4.68"  "1.1e-05" "1.280889e-03"
26  "   13"   " 3"        " 0.02"  "1.2e-06" "6.288000e-04"
110 "  143"   " 6"        " 0.24"  "1.2e-07" "1.257600e-04"
101 "   38"   " 3"        " 0.06"  "3.5e-05" "3.334545e-03"
111 "   38"   " 3"        " 0.06"  "3.5e-05" "3.334545e-03"
121 "   40"   " 3"        " 0.07"  "4.1e-05" "3.580667e-03"
131 " 1361"   "10"        " 2.29"  "4.7e-05" "3.788923e-03"
31  "   20"   " 3"        " 0.03"  "4.8e-06" "1.257600e-03"
41  "   20"   " 3"        " 0.03"  "4.8e-06" "1.257600e-03"
141 "    8"   " 2"        " 0.01"  "7.6e-05" "5.689143e-03"
       LOG2.FC1        LOG2.FC2 
"transcriptome"   "translatome" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>