annoGR-class

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Class annoGR

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

Keywords
classes
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

Aliases
  • annoGR-class
  • annoGR
  • annoGR,GRanges-method
  • annoGR,TxDb-method
  • annoGR,EnsDb-method
  • info
  • info,annoGR-method
  • coerce,GRanges,annoGR-method
  • coerce,annoGR,GRanges-method
Examples
    if(interactive()){
        library(EnsDb.Hsapiens.v79)
        anno <- annoGR(EnsDb.Hsapiens.v79)
    }
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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