Last data update: 2014.03.03

 R: Funtion to fetch annotations from biomaRt.
MEDIPS.getAnnotationR Documentation

Funtion to fetch annotations from biomaRt.

Description

The function receives predifined annotations from ensembl biomaRt for subsequent annotation of a result table.

Usage

MEDIPS.getAnnotation(host="www.ensembl.org",dataset=c("hsapiens_gene_ensembl","mmusculus_gene_ensembl")[1],annotation=c("TSS","EXON","GENE")[1],tssSz=c(-1000,500),chr=NULL)

Arguments

host

BioMart database host you want to connect to. For current ensembl version, use "www.ensembl.org". For other versions, set to the respective archive host, e.g. "may2012.archive.ensembl.org" for Ensembl 67 Please ensure that the ensembl version is compatible to the used genome version.

dataset

The dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart).

annotation

Type of annotation you want to retrieve. You can select "EXON" for exonic regions, "GENE" for gene regions including introns and "TSS" for regions at the transcirption start site.

tssSz

Defines the TSS region: start and end position relative to the strand and position of the transcript.

chr

Chromosome names for which the annotations should be filtered.

Value

The MEDIPS.getAnnotation function returns a list of annotation tables where each table consists of

id

the id of the annotation

chr

the chromosome of the annotation

start

the start position (5') of the annotation

end

the end position (3') of the annotation

Author(s)

Joern Dietrich and Matthias Lienhard

Examples


#homo sapiens, current ensembl version
#annotation_hs = MEDIPS.getAnnotation(dataset="hsapiens_gene_ensembl", annotation="TSS", chr=c("chr22"),tssSz=c(-1000,500))

#mus musculus, ensembl version 58 (mm9)
annotation_mm9 = MEDIPS.getAnnotation(host="may2010.archive.ensembl.org",dataset="mmusculus_gene_ensembl", annotation="TSS", chr=c("chr19"))

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(MEDIPS)
Loading required package: BSgenome
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEDIPS/MEDIPS.getAnnotation.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MEDIPS.getAnnotation
> ### Title: Funtion to fetch annotations from biomaRt.
> ### Aliases: MEDIPS.getAnnotation
> 
> ### ** Examples
> 
> 
> #homo sapiens, current ensembl version
> #annotation_hs = MEDIPS.getAnnotation(dataset="hsapiens_gene_ensembl", annotation="TSS", chr=c("chr22"),tssSz=c(-1000,500))
> 
> #mus musculus, ensembl version 58 (mm9)
> annotation_mm9 = MEDIPS.getAnnotation(host="may2010.archive.ensembl.org",dataset="mmusculus_gene_ensembl", annotation="TSS", chr=c("chr19"))
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Execution halted


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO