MEDIPS.getAnnotation: Funtion to fetch annotations from biomaRt.

In paolopavan/medips: DNA IP-seq data analysis

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"))

paolopavan/medips documentation built on May 24, 2019, 6:14 p.m.