Map FlyBase CG accession numbers with manufacturer identifiers

Description

indacFLYBASE is an R object that contains mappings between manufacturer identifiers and FlyBase CG accession numbers. These accessions are used by Ensembl and supported by FlyBase.

Details

This object is a simple mapping of manufacturer identifiers http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene to Flybase CG Accession Numbers.

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 <- indacFLYBASECG
# Get the manufacturer IDs that are mapped to a Flybase CG ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the FlyBase CG IDs for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}
#For the reverse map FLYBASECG2EG:
# Convert to a list
xx <- as.list(indacFLYBASECG2PROBE)
if(length(xx) > 0){
   # Gets the manufacturer IDs for the first five FlyBase CG IDs
   xx[1:5]
   # Get the first one
   xx[[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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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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(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/indacFLYBASECG.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indacFLYBASECG
> ### Title: Map FlyBase CG accession numbers with manufacturer identifiers
> ### Aliases: indacFLYBASECG indacFLYBASECG2PROBE
> ### 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 <- indacFLYBASECG
> # Get the manufacturer IDs that are mapped to a Flybase CG ID
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+   # Get the FlyBase CG IDs for the first five genes
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
[1] "CG9075"
> #For the reverse map FLYBASECG2EG:
> # Convert to a list
> xx <- as.list(indacFLYBASECG2PROBE)
> if(length(xx) > 0){
+    # Gets the manufacturer IDs for the first five FlyBase CG IDs
+    xx[1:5]
+    # Get the first one
+    xx[[1]]
+ }
[1] "1000037644"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>