ChIPpeakAnno (version 3.6.4)

annoGR-class: Class annoGR

Description

An object of class annoGR represents the annotation data could be used by annotationPeakInBatch.

Usage

## S3 method for class 'GRanges':
annoGR(ranges, feature="group", date, ...)
    ## S3 method for class 'TxDb':
annoGR(ranges, feature=c(
                            "gene", "transcript", "exon",
                            "CDS", "fiveUTR", "threeUTR",
                            "microRNA", "tRNAs", "geneModel"),
                   date, source, mdata, OrganismDb)
    ## S3 method for class 'EnsDb':
annoGR(ranges, 
                   feature=c("gene", "transcript", "exon", "disjointExons"),
                   date, source, mdata)

Arguments

ranges

an object of GRanges, TxDb or EnsDb

feature

annotation type

date

a Date object

...

could be following parameters

source

character, where the annotation comes from

mdata

data frame, metadata from annotation

OrganismDb

an object of OrganismDb. It is used for extracting gene symbol for geneModel group for TxDb

Objects from the Class

Objects can be created by calls of the form new("annoGR", date, elementMetadata, feature, mdata, ranges, seqinfo, seqnames, source, strand)

Examples

if(interactive()){
        library(EnsDb.Hsapiens.v79)
        anno <- annoGR(EnsDb.Hsapiens.v79)
    }