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Last data update: 2014.03.03

R: Class 'annoGR'

annoGR-class

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(interactive()){
        library(EnsDb.Hsapiens.v79)
        anno <- annoGR(EnsDb.Hsapiens.v79)
    }

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/annoGR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: annoGR-class
> ### Title: Class 'annoGR'
> ### 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
> ### Keywords: classes
> 
> ### ** Examples
> 
> #    if(interactive()){
>         library(EnsDb.Hsapiens.v79)
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

>         anno <- annoGR(EnsDb.Hsapiens.v79)
> #    }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Class annoGR