R: Annotation of GO Identifiers to their Cellular Component...
GOCCOFFSPRING
R Documentation
Annotation of GO Identifiers to their Cellular Component Offspring
Description
This data set describes associations between GO molecular function (MF)
terms and their offspring MF terms, based on the directed acyclic
graph (DAG) defined by the Gene Ontology Consortium. The format is an R
object mapping the GO MF terms to all offspring terms, where an
offspring term is a more specific GO term that is preceded
by the given GO term in the DAG (in other words, the children and all
their children, etc.).
Details
Each GO CC term is mapped to a vector of offspring GO MF terms.
Cellular component is defined as the subcellular structures,
locations, and macromolecular complexes; examples include nucleus,
telomere, and origin recognition complex as defined b y Gene Ontology
Consortium.
Mappings were based on data provided: Gene Ontology
ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
With a date stamp from the source of: 20160305
AnnotationDb-class for use of
the select() interface.
Examples
## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.
## Bimap interface:
# Convert the object to a list
xx <- as.list(GOCCOFFSPRING)
# Remove GO identifiers that do not have any offspring
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
# Get the offspring GO identifiers for the first two elents of xx
goidentifiers <- xx[1:2]
}
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.
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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(GO.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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GO.db/GOCCOFFSPRING.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOCCOFFSPRING
> ### Title: Annotation of GO Identifiers to their Cellular Component
> ### Offspring
> ### Aliases: GOCCOFFSPRING
> ### Keywords: datasets
>
> ### ** Examples
>
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
>
> ## Bimap interface:
> # Convert the object to a list
> xx <- as.list(GOCCOFFSPRING)
> # Remove GO identifiers that do not have any offspring
> xx <- xx[!is.na(xx)]
> if(length(xx) > 0){
+ # Get the offspring GO identifiers for the first two elents of xx
+ goidentifiers <- xx[1:2]
+ }
>
>
>
>
>
> dev.off()
null device
1
>