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

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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 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.

Note that the version of the annotation db must match with the genome used for mapping because the coordinates may differ for different genome releases. For example, if you are using Mus_musculus.v103 for mapping, you'd best also use EnsDb.Mmusculus.v103 for annotation. See Examples for more info.

Author(s)

Lihua Julie Zhu, Jianhong Ou, Kai Hu

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() || Sys.getenv("USER")=="jianhongou" )
{
  library(biomaRt)
  mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
  Annotation <- getAnnotation(mart, featureType="TSS")
}

##########################################################
#  Below are 3 options to fetch the annotation file.     #
##########################################################
if (interactive() || Sys.getenv("USER")=="jianhongou" ){
## Option1: with the AnnotationHub package
library(AnnotationHub)
ah <- AnnotationHub()
EnsDb.Mmusculus <- query(ah, pattern = c("Mus musculus", "EnsDb"))
EnsDb.Mmusculus.v101 <- EnsDb.Mmusculus[[length(EnsDb.Mmusculus)]]
class(EnsDb.Mmusculus.v101)

## Option2: with the getAnnotation() function
library(ChIPpeakAnno)
library(biomaRt)
listMarts()
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", 
                dataset="mmusculus_gene_ensembl")
Annotation <- getAnnotation(mart)
# Note that getAnnotation() queries biomart, which is always up-to-date.

## Option3: build your own EnsDb package
## This may need extra effort, and the ?makeEnsembldbPackage 
## is a good starting point.
}

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.