ChIPpeakAnno (version 3.6.5)

getAnnotation: Obtain the TSS, exon or miRNA annotation for the specified species

Description

Obtain the TSS, exon or miRNA annotation for the specified species using the biomaRt package

Usage

getAnnotation(mart,  featureType=c("TSS","miRNA", "Exon", "5utr", "3utr",  "ExonPlusUtr", "transcript"))

Arguments

mart

A mart object, see useMart of biomaRt package for details.

featureType

TSS, miRNA, Exon, 5'UTR, 3'UTR, transcript or Exon plus UTR. The default is TSS.

Value

GRanges or RangedData with slot start holding the start position of the feature, slot end holding the end position of the feature, slot names holding the id of the feature, slot space holding the chromosome location where the feature is located. In addition, the following variables are included.

strand

1 for positive strand and -1 for negative strand where the feature is located

description

description of the feeature such as gene

References

Durinck S. et al. (2005) BioMart and Bioconductor: a powerful link between biological biomarts and microarray data analysis. Bioinformatics, 21, 3439-3440.

Examples

if (interactive())
{
  mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
  Annotation <- getAnnotation(mart, featureType="TSS")
}