getAnnotation {ChIPpeakAnno} | R Documentation

## 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

### Note

For featureType of TSS, start is the transcription start site if strand is 1 (plus strand), otherwise, end is the transcription start site

### Author(s)

Lihua Julie Zhu, Jianhong Ou

### 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")
    }

[Package ChIPpeakAnno version 3.12.7 Index]