Get all available KEGG annotations and InterPro domains for a set of
entrezgene identifiers from the KEGG annotation package and
from the ensembl biomaRt.
Character vector of entrezgene identifiers. This is
the global universe of genes to test against.
pathways
Optional character vector of KEGG pathway
identifiers. This can be used in order to test for
over-representation of only a subset of all the available KEGG
pathways.
ensemblMart
Character giving the type of Biomart to
use. Defaults to Human Ensembl.
Details
This function is a wrapper around the KEGG annotation
package and a customized query of the ensembl biomaRt
database. For the gene identifiers in universe and all or a
selection of KEGG pathways it will fetch the necessary information and
create an object of class ipDataSource which can later be used
as input to gseDomain
Value
An object of class ipDataSource.
Author(s)
Florian Hahne
See Also
gseDomain
Examples
if(interactive())
getKEGGdata()
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.
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(domainsignatures)
Loading required package: KEGG.db
Loading required package: AnnotationDbi
Loading required package: stats4
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: 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: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
Loading required package: prada
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase
Attaching package: 'robustbase'
The following object is masked from 'package:Biobase':
rowMedians
Scalable Robust Estimators with High Breakdown Point (version 1.3-11)
Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/domainsignatures/getKEGGdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getKEGGdata
> ### Title: Fetch KEGG annotations and InterPro domains
> ### Aliases: getKEGGdata
> ### Keywords: IO
>
> ### ** Examples
>
> #if(interactive())
> getKEGGdata()
object of class 'ipDataSource' containing mapping data
for type 'KEGG' pathways
229 pathways with 5894 genes
and 4909 annotated InterPro domains
>
>
>
>
>
> dev.off()
null device
1
>