R: Map between Manufacturer IDs and Gene Ontology (GO)
illuminaHumanv2BeadIDGO
R Documentation
Map between Manufacturer IDs and Gene Ontology (GO)
Description
illuminaHumanv2BeadIDGO is an R object that provides mappings between
manufacturer identifiers and the GO identifiers that they are
directly associated with.
Details
Each Entrez 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 Entrez Gene
id. 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
Mappings between probe identifiers and GO information were obtained through
their mappings to Entrez Gene identifiers. NAs are assigned to probe 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: 20100904
Examples
x <- illuminaHumanv2BeadIDGO
# Get the probe identifiers that are mapped to a GO ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Try the firest one
got <- xx[[1]]
got[[1]][["GOID"]]
got[[1]][["Ontology"]]
got[[1]][["Evidence"]]
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(illuminaHumanv2BeadID.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
Loading required package: org.Hs.eg.db
illuminaHumanv2BeadID.db is an older package, and the package
contributor no longer supports it. Please be advised that this
package is now out of date and should not occur in future
bioconductor releases. For a more current package containing the
same kind of data, please use the appropriate illumina_XXX_.db
packages instead of the illumina_XXX_BeadID.db packages and make use
of the new illumina_XXX_ARRAYADDRESS mapping to convert between
BeadIDs and Illumina IDs.
*_XXX_ here refers to the species and version for this platform
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaHumanv2BeadID.db/illuminaHumanv2BeadIDGO.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2BeadIDGO
> ### Title: Map between Manufacturer IDs and Gene Ontology (GO)
> ### Aliases: illuminaHumanv2BeadIDGO
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaHumanv2BeadIDGO
> # Get the probe identifiers that are mapped to a GO ID
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Try the firest one
+ got <- xx[[1]]
+ got[[1]][["GOID"]]
+ got[[1]][["Ontology"]]
+ got[[1]][["Evidence"]]
+
+ }
[1] "IEA"
>
>
>
>
>
> dev.off()
null device
1
>