org.At.tairGO is an R object that provides mappings between TAIR
identifiers and the GO identifiers that they are directly associated
with. This mapping and its reverse mapping do NOT associate the child
terms from the GO ontology with the gene. Only the directly evidenced
terms are represented here.
Details
Each TAIR Gene identifier is mapped to a list of lists. The names on
the outer list are GO identifiers. Each inner list consists of three
named elements: GOID, Ontology, and Evidence.
The GOID element matches the GO identifier named in the outer list and is
included for convenience when processing the data using 'lapply'.
The Ontology element indicates which of the three Gene Ontology
categories this identifier belongs to. The categories are
biological process (BP), cellular component (CC), and molecular
function (MF).
The Evidence element contains a code indicating what kind of
evidence supports the association of the GO identifier to the TAIR Gene
id. Some of the evidence codes in use include:
IMP: inferred from mutant phenotype
IGI: inferred from genetic interaction
IPI: inferred from physical interaction
ISS: inferred from sequence similarity
IDA: inferred from direct assay
IEP: inferred from expression pattern
IEA: inferred from electronic annotation
TAS: traceable author statement
NAS: non-traceable author statement
ND: no biological data available
IC: inferred by curator
A more complete listing of evidence codes can be found at:
Mappings between TAIR gene identifiers and GO information were
obtained through their mappings to TAIR gene identifiers. NAs are
assigned to TAIR identifiers that can not be mapped to any Gene
Ontology information. Mappings between Gene Ontology identifiers an
Gene Ontology terms and other information are available in a separate
data package named GO.
Mappings were based on data provided by: Gene Ontology
ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
With a date stamp from the source of: 20160305
For the reverse map GO2TAIR, each GO term maps to a named vector of TAIR
gene identifiers. A GO identifier may be mapped to the same TAIR
identifier more than once but the evidence code can be
different. Mappings between Gene Ontology identifiers and Gene
Ontology terms and other information are available in a separate data
package named GO.
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:
x <- org.At.tairGO
# Get the TAIR gene identifiers that are mapped to a GO ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
# Try the first one
got <- xx[[1]]
got[[1]][["GOID"]]
got[[1]][["Ontology"]]
got[[1]][["Evidence"]]
}
# For the reverse map:
# Convert to a list
xx <- as.list(org.At.tairGO2TAIR)
if(length(xx) > 0){
# Gets the TAIR gene ids for the top 2nd and 3nd GO identifiers
goids <- xx[2:3]
# Gets the TAIR ids for the first element of goids
goids[[1]]
# Evidence code for the mappings
names(goids[[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.
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(org.At.tair.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/org.At.tair.db/org.At.tairGO.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.At.tairGO
> ### Title: Map between TAIR IDs and Gene Ontology (GO)
> ### Aliases: org.At.tairGO org.At.tairGO2TAIR
> ### 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:
> x <- org.At.tairGO
> # Get the TAIR gene identifiers that are mapped to a GO ID
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+ # Try the first one
+ got <- xx[[1]]
+ got[[1]][["GOID"]]
+ got[[1]][["Ontology"]]
+ got[[1]][["Evidence"]]
+ }
[1] "RCA"
> # For the reverse map:
> # Convert to a list
> xx <- as.list(org.At.tairGO2TAIR)
> if(length(xx) > 0){
+ # Gets the TAIR gene ids for the top 2nd and 3nd GO identifiers
+ goids <- xx[2:3]
+ # Gets the TAIR ids for the first element of goids
+ goids[[1]]
+ # Evidence code for the mappings
+ names(goids[[1]])
+ }
[1] "RCA" "RCA" "RCA" "RCA" "RCA" "RCA" "IMP" "RCA" "RCA" "RCA" "IGI" "IGI"
[13] "RCA" "IGI" "IGI" "IMP" "RCA" "RCA"
>
>
>
>
>
> dev.off()
null device
1
>