Last data update: 2014.03.03

R: Map Manufacturer identifiers to Accession Numbers
indacACCNUMR Documentation

Map Manufacturer identifiers to Accession Numbers

Description

indacACCNUM 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-Sep27

See Also

  • 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 <- indacACCNUM
# 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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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(indac.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.Dm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/indac.db/indacACCNUM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indacACCNUM
> ### Title: Map Manufacturer identifiers to Accession Numbers
> ### Aliases: indacACCNUM
> ### 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 <- indacACCNUM
> # 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] "Z49777"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>