MicroRNA IDs to Chromosomes

Description

mirbaseCHR is an R object that provides mappings between microRNA identifiers and the chromosome that contains the microRNA of interest.

Details

Each microRNA identifier maps to a vector of character strings representing possibly multiple chromosomes.

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

Examples

    x <- mirbaseCHR
    # Get the microRNA identifiers that are mapped to a chromosome
    mapped_keys <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_keys])
    if(length(xx) > 0) {
        # Get the CHR 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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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(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/mirbaseCHR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbaseCHR
> ### Title: MicroRNA IDs to Chromosomes
> ### Aliases: mirbaseCHR
> ### Keywords: data
> 
> ### ** Examples
> 
>     x <- mirbaseCHR
>     # Get the microRNA identifiers that are mapped to a chromosome
>     mapped_keys <- mappedkeys(x)
>     # Convert to a list
>     xx <- as.list(x[mapped_keys])
>     if(length(xx) > 0) {
+         # Get the CHR for the first five entries
+         xx[1:5]
+     }
$`aae-mir-2765`
[1] "supercont1.1"

$`aae-mir-999`
[1] "supercont1.100"

$`aae-mir-993`
[1] "supercont1.1056"

$`aae-mir-932`
[1] "supercont1.1064"

$`aae-mir-308`
[1] "supercont1.107"

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