getAnnotation

0th

Percentile

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

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

Keywords
misc
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

References

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

Aliases
  • getAnnotation
Examples
if (interactive())
{
  mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
  Annotation <- getAnnotation(mart, featureType="TSS")
}
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

Community examples

Looks like there are no examples yet.