annoGR-class {ChIPpeakAnno} | R Documentation

## Class `annoGR`

### Description

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

### Usage

        ## S4 method for signature 'GRanges'
    annoGR(ranges, feature="group", date, ...)
        ## S4 method for signature 'TxDb'
    annoGR(ranges, feature=c(
                                "gene", "transcript", "exon",
                                "CDS", "fiveUTR", "threeUTR",
                                "microRNA", "tRNAs", "geneModel"),
                       date, source, mdata, OrganismDb)
        ## S4 method for signature '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)`

### 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

### Author(s)

Jianhong Ou

### Examples

        if(Sys.getenv("USER")=="jianhongou"){
            library(EnsDb.Hsapiens.v79)
            anno <- annoGR(EnsDb.Hsapiens.v79)
        }

[Package ChIPpeakAnno version 3.14.2 Index]