mirbaseCONTEXT is an R object that maps microRNA identifiers to
information related to overlapping transcripts.
Details
Each microRNA identifier maps to a mirnaContext object that has 6
slots:
contextTranscriptID: Transcript identifer
contextOverlapSense: Strand of transcript
contextOverlapType: Type of overlap (exon, intron, 3' or 5' UTR)
contextNumber: Type of overlap number (eg exon 3)
contextTranscriptSource: Transcript database
contextTranscriptName: Transcript Name
Source: miRBase (Version: 19)
ftp://mirbase.org/pub/mirbase/CURRENT/
With a date stamp from the source of: 01 Aug 2012
See Also
mirnaContext
Examples
x <- mirbaseCONTEXT
# Get the CONTEXT for the first element mapped
get(mappedkeys(x)[1], x)
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/mirbaseCONTEXT.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbaseCONTEXT
> ### Title: MicroRNA IDs to Genomic Context
> ### Aliases: mirbaseCONTEXT
> ### Keywords: data
>
> ### ** Examples
>
> x <- mirbaseCONTEXT
> # Get the CONTEXT for the first element mapped
> get(mappedkeys(x)[1], x)
[+]
ENSACAT00000019163; exon (1)
>
>
>
>
>
> dev.off()
null device
1
>