Sample topGOdata and topGOresult objects

Description

The GOdata contains an instance of a topGOdata object. It can be used to run an enrichment analysis directly.

The resultFisher contains the results of an enrichment analysis.

Usage

data(GOdata)

Source

Generated using the ALL gene expression data. See topGOdata-class for code examples on how-to generate such an object.

Examples

data(GOdata)

## print the object
GOdata

data(results.tGO)

## print the object
resultFisher

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(topGO)
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 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: graph
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")'.

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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/topGO/GOdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOdata
> ### Title: Sample topGOdata and topGOresult objects
> ### Aliases: GOdata resultFisher resultKS
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(GOdata)
> 
> ## print the object
> GOdata

------------------------- topGOdata object -------------------------

 Description:
   -  Simple topGOdata object 

 Ontology:
   -  BP 

 323 available genes (all genes from the array):
   - symbol:  1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at  ...
   - score :  1 1 0.62238 0.541224 1  ...
   - 50  significant genes. 

 318 feasible genes (genes that can be used in the analysis):
   - symbol:  1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at  ...
   - score :  1 1 0.62238 0.541224 1  ...
   - 50  significant genes. 

 GO graph (nodes with at least  5  genes):
   - a graph with directed edges
   - number of nodes = 777 
   - number of edges = 1557 

------------------------- topGOdata object -------------------------

> 
> data(results.tGO)
> 
> ## print the object
> resultFisher

Description: Simple topGOdata object 
Ontology: BP 
'classic' algorithm with the 'fisher' test
777 GO terms scored: 48 terms with p < 0.01
Annotation data:
    Annotated genes: 318 
    Significant genes: 50 
    Min. no. of genes annotated to a GO: 5 
    Nontrivial nodes: 590 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>