annoGR: Class 'annoGR'

Description Usage Arguments Slots Objects from the Class Author(s) Examples

Description

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

Usage

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## 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

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

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.