ChIPpeakAnno (version 3.6.5)

annoGR-class: Class annoGR

Description

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

Usage

"annoGR"(ranges, feature="group", date, ...) "annoGR"(ranges, feature=c( "gene", "transcript", "exon", "CDS", "fiveUTR", "threeUTR", "microRNA", "tRNAs", "geneModel"), date, source, mdata, OrganismDb) "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)

Slots

seqnames, ranges, strand, elementMetadata, seqinfo

slots inherit from GRanges. The ranges must have unique names.

source

character, where the annotation comes from

date

a Date object

feature

annotation type, could be "gene", "exon", "transcript", "CDS", "fiveUTR", "threeUTR", "microRNA", "tRNAs", "geneModel" for TxDb object, or "gene", "exon" "transcript" for EnsDb object

mdata

data frame, metadata from annotation

Coercion

as(from, "annoGR"): Creates a annoGR object from a GRanges object.

as(from, "GRanges"): Create a GRanges object from a annoGR object.

Methods

info

Print basic info for annoGR object

annoGR("TxDb"), annoGR("EnsDb")

Create a annoGR object from TxDb or EnsDb object

Examples

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