MicroRNA IDs to Chromosomal Location

Description

mirbaseCHRLOC is an R object that maps microRNA identifiers to the starting position of the microRNA. The position of a microRNA 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 microRNA instead of the start.

Details

Each microRNA 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 microRNAs have multiple start sites, this field can map to multiple locations.

Source: miRBase (Version: 19) ftp://mirbase.org/pub/mirbase/CURRENT/ With a date stamp from the source of: 01 Aug 2012

Examples

    x <- mirbaseCHRLOC
    # Get the microRNA identifiers that are mapped to chromosome locations
    mapped_keys <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_keys])
    if(length(xx) > 0) {
        # Get the CHRLOC for the first five entries
        xx[1:5]
    }

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 'demo()' for some demos, 'help()' for on-line help, or
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> library(mirbase.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/mirbase.db/mirbaseCHRLOC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbaseCHRLOC
> ### Title: MicroRNA IDs to Chromosomal Location
> ### Aliases: mirbaseCHRLOC mirbaseCHRLOCEND
> ### Keywords: data
> 
> ### ** Examples
> 
>     x <- mirbaseCHRLOC
>     # Get the microRNA identifiers that are mapped to chromosome locations
>     mapped_keys <- mappedkeys(x)
>     # Convert to a list
>     xx <- as.list(x[mapped_keys])
>     if(length(xx) > 0) {
+         # Get the CHRLOC for the first five entries
+         xx[1:5]
+     }
$`aae-mir-2765`
supercont1.1 
     5248294 

$`aae-mir-999`
supercont1.100 
       2315100 

$`aae-mir-993`
supercont1.1056 
         256781 

$`aae-mir-932`
supercont1.1064 
        -154098 

$`aae-mir-308`
supercont1.107 
        508970 

> 
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> 
> dev.off()
null device 
          1 
>