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Last data update: 2014.03.03

R: Produces an object allowing to perform GO-like enrichment of...

topAnat

R Documentation

Produces an object allowing to perform GO-like enrichment of anatomical terms using the topGO package

Description

This function produces a topAnatObject, ready to use for gene set enrichment testing using functions from the topGO package. This object uses the Uberon ontology instead of the GO ontology.

Usage

topAnat(topAnatData, geneList, nodeSize = 10, ...)

Arguments

`topAnatData`	a list including a gene2anatomy list, an organ.relationships list and an organ.names data.frame, produced by the function loadTopAnatData().
`geneList`	Vector indicating foreground and background genes. Names of the vector indicate the background genes. Values are 1 (gene in foreground) or 0 (gene not in foreground).
`nodeSize`	Minimum number of genes mapped to a node for it to be tested. Default is 10.
`...`	Additional parameters as passed to build topGOdata object in topGO package.

Details

To perform the enrichment test for expression in anatomical structures for each term of Uberon ontology (browsable at http://www.ontobee.org/ontology/UBERON), the data are formatted to use the topGO package for testing. This package is interesting because it propagates the mapping of gene to terms to parent terms, and it possesses a pannel of enrichment tests and decorrelation methods. Expert users should be able to use information from the topAnatObject to test enrichment with other packages than topGO.

Value

topAnatObject, a topGO-compatible object ready for gene set enrichment testing.

Author(s)

Julien Roux julien.roux@unil.ch.

Examples

{
  myTopAnatData <- loadTopAnatData(species = "10090", datatype = "rna_seq")
  geneList <- as.factor(c(rep(0, times=90), rep(1, times=10)))
  names(geneList) <- c("ENSMUSG00000064370", "ENSMUSG00000064368", "ENSMUSG00000064367",
                    "ENSMUSG00000064363", "ENSMUSG00000065947", "ENSMUSG00000064360",
                    "ENSMUSG00000064358", "ENSMUSG00000064357", "ENSMUSG00000064356",
                    "ENSMUSG00000064354", "ENSMUSG00000064351", "ENSMUSG00000064345",
                    "ENSMUSG00000064341", "ENSMUSG00000029757", "ENSMUSG00000079941",
                    "ENSMUSG00000053367", "ENSMUSG00000016626", "ENSMUSG00000037816",
                    "ENSMUSG00000036781", "ENSMUSG00000022519", "ENSMUSG00000079606",
                    "ENSMUSG00000068966", "ENSMUSG00000038608", "ENSMUSG00000047473",
                    "ENSMUSG00000038542", "ENSMUSG00000025386", "ENSMUSG00000028145",
                    "ENSMUSG00000024816", "ENSMUSG00000020978", "ENSMUSG00000055373",
                    "ENSMUSG00000038155", "ENSMUSG00000046408", "ENSMUSG00000030032",
                    "ENSMUSG00000042249", "ENSMUSG00000071909", "ENSMUSG00000039670",
                    "ENSMUSG00000032501", "ENSMUSG00000054252", "ENSMUSG00000068071",
                    "ENSMUSG00000067578", "ENSMUSG00000074892", "ENSMUSG00000027905",
                    "ENSMUSG00000058216", "ENSMUSG00000078754", "ENSMUSG00000062101",
                    "ENSMUSG00000043633", "ENSMUSG00000071350", "ENSMUSG00000021639",
                    "ENSMUSG00000059113", "ENSMUSG00000049115", "ENSMUSG00000053310",
                    "ENSMUSG00000043832", "ENSMUSG00000063767", "ENSMUSG00000026775",
                    "ENSMUSG00000038537", "ENSMUSG00000078716", "ENSMUSG00000096820",
                    "ENSMUSG00000075089", "ENSMUSG00000049971", "ENSMUSG00000014303",
                    "ENSMUSG00000056054", "ENSMUSG00000033082", "ENSMUSG00000020801",
                    "ENSMUSG00000030590", "ENSMUSG00000026188", "ENSMUSG00000014301",
                    "ENSMUSG00000073491", "ENSMUSG00000014529", "ENSMUSG00000036960",
                    "ENSMUSG00000058748", "ENSMUSG00000047388", "ENSMUSG00000002204",
                    "ENSMUSG00000034285", "ENSMUSG00000109129", "ENSMUSG00000035275",
                    "ENSMUSG00000051184", "ENSMUSG00000034424", "ENSMUSG00000041828",
                    "ENSMUSG00000029416", "ENSMUSG00000030468", "ENSMUSG00000029911",
                    "ENSMUSG00000055633", "ENSMUSG00000027495", "ENSMUSG00000029624",
                    "ENSMUSG00000045518", "ENSMUSG00000074259", "ENSMUSG00000035228",
                    "ENSMUSG00000038533", "ENSMUSG00000030401", "ENSMUSG00000014602",
                    "ENSMUSG00000041827", "ENSMUSG00000042345", "ENSMUSG00000028530",
                    "ENSMUSG00000038722", "ENSMUSG00000075088", "ENSMUSG00000039629",
                    "ENSMUSG00000067567", "ENSMUSG00000057594", "ENSMUSG00000005907",
                   "ENSMUSG00000027496")
  myTopAnatObject <- topAnat(myTopAnatData, geneList, nodeSize=1)
}

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 'license()' or 'licence()' for distribution details.

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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
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Type 'q()' to quit R.

> library(BgeeDB)
Loading required package: 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

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:S4Vectors':

    expand

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BgeeDB/topAnat.Rd_%03d_medium.png", width=480, height=480)
> ### Name: topAnat
> ### Title: Produces an object allowing to perform GO-like enrichment of
> ###   anatomical terms using the topGO package
> ### Aliases: topAnat
> 
> ### ** Examples
> 
> {
+   myTopAnatData <- loadTopAnatData(species = "10090", datatype = "rna_seq")
+   geneList <- as.factor(c(rep(0, times=90), rep(1, times=10)))
+   names(geneList) <- c("ENSMUSG00000064370", "ENSMUSG00000064368", "ENSMUSG00000064367",
+                     "ENSMUSG00000064363", "ENSMUSG00000065947", "ENSMUSG00000064360",
+                     "ENSMUSG00000064358", "ENSMUSG00000064357", "ENSMUSG00000064356",
+                     "ENSMUSG00000064354", "ENSMUSG00000064351", "ENSMUSG00000064345",
+                     "ENSMUSG00000064341", "ENSMUSG00000029757", "ENSMUSG00000079941",
+                     "ENSMUSG00000053367", "ENSMUSG00000016626", "ENSMUSG00000037816",
+                     "ENSMUSG00000036781", "ENSMUSG00000022519", "ENSMUSG00000079606",
+                     "ENSMUSG00000068966", "ENSMUSG00000038608", "ENSMUSG00000047473",
+                     "ENSMUSG00000038542", "ENSMUSG00000025386", "ENSMUSG00000028145",
+                     "ENSMUSG00000024816", "ENSMUSG00000020978", "ENSMUSG00000055373",
+                     "ENSMUSG00000038155", "ENSMUSG00000046408", "ENSMUSG00000030032",
+                     "ENSMUSG00000042249", "ENSMUSG00000071909", "ENSMUSG00000039670",
+                     "ENSMUSG00000032501", "ENSMUSG00000054252", "ENSMUSG00000068071",
+                     "ENSMUSG00000067578", "ENSMUSG00000074892", "ENSMUSG00000027905",
+                     "ENSMUSG00000058216", "ENSMUSG00000078754", "ENSMUSG00000062101",
+                     "ENSMUSG00000043633", "ENSMUSG00000071350", "ENSMUSG00000021639",
+                     "ENSMUSG00000059113", "ENSMUSG00000049115", "ENSMUSG00000053310",
+                     "ENSMUSG00000043832", "ENSMUSG00000063767", "ENSMUSG00000026775",
+                     "ENSMUSG00000038537", "ENSMUSG00000078716", "ENSMUSG00000096820",
+                     "ENSMUSG00000075089", "ENSMUSG00000049971", "ENSMUSG00000014303",
+                     "ENSMUSG00000056054", "ENSMUSG00000033082", "ENSMUSG00000020801",
+                     "ENSMUSG00000030590", "ENSMUSG00000026188", "ENSMUSG00000014301",
+                     "ENSMUSG00000073491", "ENSMUSG00000014529", "ENSMUSG00000036960",
+                     "ENSMUSG00000058748", "ENSMUSG00000047388", "ENSMUSG00000002204",
+                     "ENSMUSG00000034285", "ENSMUSG00000109129", "ENSMUSG00000035275",
+                     "ENSMUSG00000051184", "ENSMUSG00000034424", "ENSMUSG00000041828",
+                     "ENSMUSG00000029416", "ENSMUSG00000030468", "ENSMUSG00000029911",
+                     "ENSMUSG00000055633", "ENSMUSG00000027495", "ENSMUSG00000029624",
+                     "ENSMUSG00000045518", "ENSMUSG00000074259", "ENSMUSG00000035228",
+                     "ENSMUSG00000038533", "ENSMUSG00000030401", "ENSMUSG00000014602",
+                     "ENSMUSG00000041827", "ENSMUSG00000042345", "ENSMUSG00000028530",
+                     "ENSMUSG00000038722", "ENSMUSG00000075088", "ENSMUSG00000039629",
+                     "ENSMUSG00000067567", "ENSMUSG00000057594", "ENSMUSG00000005907",
+                    "ENSMUSG00000027496")
+   myTopAnatObject <- topAnat(myTopAnatData, geneList, nodeSize=1)
+ }

Warning: an organ relationships file was found in the working directory and will be used as is. Please delete and rerun the function if you want the data to be updated.

Warning: an organ names file was found in the working directory and will be used as is. Please delete and rerun the function if you want the data to be updated.

Warning: a gene to organs mapping file was found in the working directory and will be used as is. Please delete and rerun the function if you want the data to be updated.

Parsing the results...............................................

Adding BGEE:0 as unique root of all terms of the ontology.........

Done.

Checking topAnatData object.........

Checking gene list..................
Warning: Some genes in your gene list have no expression data in Bgee, and will not be included in the analysis.  92  genes in background will be kept.

Building 'most specific' Terms......  ( 20 Terms found. )

Build DAG topology..................  ( 192 terms and 322 relations. )

Annotating nodes (Can be long)......  ( 92 genes annotated to the nodes. )
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>