annoGR: Class 'annoGR'

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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)
    }

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.