R: Map Manufacturer identifiers to Accession Numbers
illuminaHumanv3ACCNUM
R Documentation
Map Manufacturer identifiers to Accession Numbers
Description
illuminaHumanv3ACCNUM is an R object that contains mappings between a
manufacturer's identifiers and manufacturers accessions.
Details
For chip packages such as this, the ACCNUM mapping comes directly from
the manufacturer. This is different from other mappings which are
mapped onto the probes via an Entrez Gene identifier.
Each manufacturer identifier maps to a vector containing a GenBank accession number.
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: 2015-Mar17
Examples
x <- illuminaHumanv3ACCNUM
# Get the probe identifiers that are mapped to an ACCNUM
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the ACCNUM 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(illuminaHumanv3.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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaHumanv3.db/illuminaHumanv3ACCNUM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaHumanv3ACCNUM
> ### Title: Map Manufacturer identifiers to Accession Numbers
> ### Aliases: illuminaHumanv3ACCNUM
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- illuminaHumanv3ACCNUM
> # Get the probe identifiers that are mapped to an ACCNUM
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the ACCNUM for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "NM_001402"
>
>
>
>
>
> dev.off()
null device
1
>