Entrez Gene IDs to Chromosomal Location

Description

org.Dm.egCHRLOC is an R object that maps entrez gene identifiers to the starting position of the gene. The position of a gene is measured as the number of base pairs.

The CHRLOCEND mapping is the same as the CHRLOC mapping except that it specifies the ending base of a gene instead of the start.

Details

Each entrez gene identifier maps to a named vector of chromosomal locations, where the name indicates the chromosome.

Chromosomal locations on both the sense and antisense strands are measured as the number of base pairs from the p (5' end of the sense strand) to q (3' end of the sense strand) arms. Chromosomal locations on the antisense strand have a leading "-" sign (e. g. -1234567).

Since some genes have multiple start sites, this field can map to multiple locations.

Mappings were based on data provided by: UCSC Genome Bioinformatics (Drosophila melanogaster) ftp://hgdownload.cse.ucsc.edu/goldenPath/dm6 With a date stamp from the source of: 2014-Dec12

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 <- org.Dm.egCHRLOC
# Get the entrez gene identifiers that are mapped to chromosome locations
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the CHRLOC for the first five genes
  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)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(org.Dm.eg.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


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/org.Dm.eg.db/org.Dm.egCHRLOC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Dm.egCHRLOC
> ### Title: Entrez Gene IDs to Chromosomal Location
> ### Aliases: org.Dm.egCHRLOC org.Dm.egCHRLOCEND
> ### 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 <- org.Dm.egCHRLOC
> # Get the entrez gene identifiers that are mapped to chromosome locations
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+   # Get the CHRLOC for the first five genes
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
     3R      3R 
7143486 7143728 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>