R: Map between Manufacturer Identifiers and Entrez Gene
illuminaHumanv2BeadIDENTREZID
R Documentation
Map between Manufacturer Identifiers and Entrez Gene
Description
illuminaHumanv2BeadIDENTREZID is an R object that provides mappings between
manufacturer identifiers and Entrez Gene identifiers.
Details
Each manufacturer identifier is mapped to a vector of Entrez Gene identifiers. An
NA is assigned to those manufacturer identifiers that can not be mapped
to an Entrez Gene identifier at this time.
If a given manufacturer identifier can be mapped to different Entrez Gene identifiers
from various sources, we attempt to select the common identifiers. If a
concensus cannot be determined, we select the smallest identifier.
Mappings were based on data provided by: Entrez Gene
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
With a date stamp from the source of: 2010-Sep7
x <- illuminaHumanv2BeadIDENTREZID
# Get the probe identifiers that are mapped to an ENTREZ Gene ID
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the ENTREZID for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
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/illuminaHumanv2BeadIDENTREZID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv2BeadIDENTREZID
> ### Title: Map between Manufacturer Identifiers and Entrez Gene
> ### Aliases: illuminaHumanv2BeadIDENTREZID illuminaHumanv2BeadIDLOCUSID
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaHumanv2BeadIDENTREZID
> # Get the probe identifiers that are mapped to an ENTREZ Gene ID
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the ENTREZID for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "317761"
>
>
>
>
>
> dev.off()
null device
1
>