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 'annoGR'
    info(object)

    ## 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

`object` | annoGR object.
`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

### 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

### Objects from the Class

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

### Author(s)

Jianhong Ou

### Examples

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

[Package ChIPpeakAnno version 3.24.2 Index]