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

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

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 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.

list("strand")	1 for positive strand and -1 for negative strand where the feature is located
list("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")
}

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.